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.

Time for the do gooders to butt out?:Pros and cons.

History judges Christopher Columbus.

Beyond the hagiography.

Are our schools rotting our kids' brains?

On Babylon the great:The Watchtower Society's commentary.

BABYLON THE GREAT:

Among John’s visions recorded in the book of Revelation appear pronouncements of judgment against “Babylon the Great,” as well as a description of her and of her downfall.—Re 14:8; 16:19; chaps 17, 18; 19:1-3.

In Revelation 17:3-5, Babylon the Great is described as a woman arrayed in purple and scarlet, richly adorned, and sitting upon a scarlet-colored wild beast having seven heads and ten horns. Upon her forehead a name is written, “a mystery: ‘Babylon the Great, the mother of the harlots and of the disgusting things of the earth.’” She is also depicted as sitting on “many waters” representing “peoples and crowds and nations and tongues.”—Re 17:1-15.

The luxury and the dominion attributed to Babylon the Great do not allow for simply equating her with the literal city of Babylon in Mesopotamia. After ancient Babylon fell to Cyrus the Persian in 539 B.C.E., it lost its position as a dominant world power, its captives, including the Jews, being freed. Although the city continued to exist even beyond the days of the apostles, and hence existed in John’s day, it was no longer a city of world importance, and it eventually fell into decay and utter ruin. Thus, Babylon the Great must be viewed as a symbolic city, one of which the literal city of Babylon was the prototype. Because the ancient city gives the mystic city its name, it is helpful to consider briefly the outstanding features of Babylon on the Euphrates, features that provide clues as to the identity of the symbolic city of John’s vision.

Characteristics of Ancient Babylon. The founding of the city of Babylon on the Plains of Shinar was concurrent with the attempt at building the Tower of Babel. (Ge 11:2-9) The popular cause to be advanced by the tower and city construction was, not the exaltation of God’s name, but that the builders might “make a celebrated name” for themselves. The ziggurat towers uncovered not only in the ruins of ancient Babylon but elsewhere in Mesopotamia would seem to confirm the essentially religious nature of the original tower, whatever its form or style. The decisive action taken by Jehovah God to overthrow the temple construction clearly condemns it as of a false religious origin. Whereas the Hebrew name given the city, Babel, means “Confusion,” the Sumerian name (Ka-dingir-ra) and the Akkadian name (Bab-ilu) both mean “Gate of God.” Thus the remaining inhabitants of the city altered the form of its name to avoid the original condemnatory sense, but the new or substitute form still identified the city with religion.

The Bible lists Babel first when giving the ‘beginning of Nimrod’s kingdom.’ (Ge 10:8-10) Throughout the Hebrew Scriptures the ancient city of Babylon is featured prominently as the longtime enemy of Jehovah God and his people.

Though Babylon became the capital of a political empire in the seventh and sixth centuries B.C.E., it was outstandingly prominent during its entire history as a religious center from which religious influence radiated in many directions.

Professor Morris Jastrow, Jr., in his work The Religion of Babylonia and Assyria (1898, pp. 699-701), says regarding this: “In the ancient world, prior to the rise of Christianity, Egypt, Persia, and Greece felt the influence of the Babylonian religion. . . . In Persia, the Mithra cult reveals the unmistakable influence of Babylonian conceptions; and if it be recalled what a degree of importance the mysteries connected with this cult acquired among the Romans, another link will be added connecting the ramifications of ancient culture with the civilization of the Euphrates Valley.” In conclusion he refers to “the profound impression made upon the ancient world by the remarkable manifestations of religious thought in Babylonia and by the religious activity that prevailed in that region.”

Babylon’s religious influence is traced eastward to India in the book New Light on the Most Ancient East, by archaeologist V. Childe (1957, p. 185). Among other points he states: “The swastika and the cross, common on stamps and plaques, were religious or magical symbols as in Babylonia and Elam in the earliest prehistoric period, but preserve that character also in modern India as elsewhere.” Thus, ancient Babylon’s religious influence spread out to many peoples and nations, much farther and with greater potency and endurance than did her political strength.

Like mystic Babylon, the ancient city of Babylon, in effect, sat on the waters, located, as it was, astride the Euphrates River and having various canals and water-filled moats. (Jer 51:1, 13; Re 17:1, 15) These waters served as a defense to the city, and they provided the thoroughfares upon which ships brought wealth and luxuries from many sources. Notably, the water of the Euphrates is depicted as drying up prior to Babylon the Great’s experiencing the wrath of divine judgment.—Re 16:12, 19.

Distinguishing Features of Mystic Babylon. The symbolic woman bearing the name Babylon the Great is “the great city that has a kingdom over the kings of the earth,” a kingdom that allows her, in effect, to sit on “peoples and crowds and nations and tongues.” (Re 17:1, 15, 18) A kingdom over other kingdoms and nations is what is defined as an “empire.” Babylon the Great places herself above earthly kings, exercising power and influence over them. She rides the symbolic seven-headed beast, beasts being used elsewhere in the Bible as symbols of political world powers.—See BEASTS, SYMBOLIC.

Some scholars assume that Babylon the Great is a political empire, either Babylon or Rome. We have already seen that Babylon as a political empire had long since ceased to exist when John received his prophetic vision. As to Rome, the nature of its political rule does not harmonize with the description of Babylon the Great’s course and her methods of dominating. She is a harlot, committing fornication with the kings of the earth, making them drunk with the wine of her fornication, misleading the nations by her “spiritistic practice.” (Re 17:1, 2; 18:3, 23) Rome’s dominion, by contrast, was gained and maintained by its ironlike military might and its firm application of Roman law among its provinces and colonies. Recognizing this fact, The Interpreter’s Dictionary of the Bible says: “It is not sufficient to identify Rome and Babylon. Babylon embraces more than one empire or culture. It is defined rather by dominant idolatries than by geographical or temporal boundaries. Babylon is coextensive with the kingdom of that beast which has corrupted and enslaved mankind, and whom the Lamb must conquer (Rev. 17:14) if mankind is to be freed.”—Edited by G. Buttrick, 1962, Vol. 1, p. 338.

The symbol of a harlot or a fornicatrix is used frequently in the Hebrew Scriptures. The nation of Israel was warned against entering into covenant relations with the nations of Canaan because this would lead them to commit “immoral intercourse [“play the harlot,” RS] with their gods.” (Ex 34:12-16) Both Israel and Judah apostatized from the true worship of Jehovah God and were condemned by him as having engaged in harlotry, prostituting themselves to the political nations and their gods. (Isa 1:21; Jer 3:6-10, 13; Eze 16:15-17, 28, 29, 38; Ho 6:10; 7:11; 8:9, 10) It may be noted here that God was not viewing Israel or Judah as mere political entities entering into relations with other political governments. Instead God reprimanded them on the basis of their being in a sacred covenant with him, hence responsible to be a holy people devoted to him and his pure worship.—Jer 2:1-3, 17-21.

A similar usage of this figure is found in the Christian Greek Scriptures. The Christian congregation is likened to a virgin espoused to Christ as her Head and King. (2Co 11:2; Eph 5:22-27) The disciple James warned Christians against committing spiritual adultery through friendship with the world. (Jas 4:4; compare Joh 15:19.) The fornications of Babylon the Great and her “daughters” are of a similar nature and not some unique exception. (The term “daughters” at times is employed in the Bible to refer to the suburbs or surrounding towns of a city or metropolis, as the “dependent towns” [literally, “daughters” in Hebrew] of Samaria and Sodom; see Eze 16:46-48.)

An additional significant factor is that when Babylon the Great goes down under the devastating attack of the ten horns of the symbolic wild beast, her fall is mourned by her companions in fornication, the kings of the earth, and also by the merchants and shippers who dealt with her in supplying luxurious commodities and gorgeous fineries. While these political and commercial representatives survive her desolation, notably no religious representatives are depicted as still on the scene to share in mourning her downfall. (Re 17:16, 17; 18:9-19) The kings of the earth are shown as having judgment executed upon them sometime after mystic Babylon’s annihilation, and their destruction comes, not from the “ten horns,” but from the sword of the King of kings, the Word of God.—Re 19:1, 2, 11-18.

A further distinguishing characteristic of Babylon the Great is her drunkenness, she being pictured as “drunk with the blood of the holy ones and with the blood of the witnesses of Jesus.” (Re 17:4, 6; 18:24; 19:1, 2) She thus is the spiritual counterpart of the ancient city of Babylon, expressing the same enmity toward the true people of God. Significantly, it was to the charge of religious leaders that Jesus laid the responsibility for “all the righteous blood spilled on earth, from the blood of righteous Abel to the blood of Zechariah.” While those words were addressed to religious leaders from among Jesus’ own race, the Jewish nation, and while persecution against Jesus’ followers was particularly intense from that sector for a time, history shows that thereafter the opposition to genuine Christianity came from other sources (the Jews themselves suffering considerable persecution).—Mt 23:29-35.

All the above factors are significant, and they must all be considered in arriving at a true picture of symbolic Babylon the Great and what it represents.

That pesky second law continues to bedevil abiogenesis

Thermodynamics of the Origin of Life
Brian Miller

Popular articles on origin-of-life research have often portrayed the field as constantly advancing and quickly converging on a purely materialistic explanation for the first autonomous cell. However, the true state of affairs is far grimmer. The highpoint of optimism was actually in the 1950s when Stanley Miller’s experiment produced several of the building blocks of life. Unfortunately, geologists later recognized that the gases used in that experiment did not match the chemistry of the early Earth. When redone with those actually present, the experiments produced  few building blocks in sufficient quantities to contribute to origin-of-life scenarios. Moreover, close examination of modern attempts to synthesize life’s precursors reveals that the  formation of many of them on the early Earth in significant quantities is virtually impossible. However, the more fundamental challenge of thermodynamics dwarfs even these hurdles.

Common arguments about the origin of life have traditionally focused on the unlikelihood of life forming by chance. Perhaps most famously, physicist Fred Hoyle calculated the probability of a cell coalescing to be roughly 1 part in 10 to the power of 40,000. He compared this probability to the chances of a  tornado plowing through a junkyard and assembling a jet airplane. The concept of probability is closely linked to that of entropy, since probability is proportional to the number of configurations (N) in which some state could occur, and  entropy is proportional to the log of N. As an example, the number of ways water molecules can arrange themselves in the solid state is much smaller than the number ways in the liquid or gas states, so ice is the state with the lowest entropy. Due to this connection, the probability argument is often restated that nature tends to move from states of lower entropy to higher entropy, which simply means that nature moves towards states which are highly probable. This tendency is known as the second law of thermodynamics.

Such arguments sound impressive at first, but they are actually incomplete. Nearly all researchers recognize that the first cell could not have come about by chance. They instead believe that some physical processes helped to beat the odds. As an analogy, one could never role one thousand sixes in a row with fair dice. However, if the dice were loaded, that outcome could be quite likely or even close to guaranteed. Analogously, some systems do, in fact, naturally move from states of higher entropy to those of lower entropy (i.e., seemingly low probability) if the lower-entropy states are highly biased to occur. Such a bias is created by a second driving tendency. Namely, nature tends to move from states of higher energy to those of lower energy. For instance, rocks roll downhill, since lower altitude corresponds to lower gravitational energy. Likewise, molecules of water attract each other, so ice is a lower energy state since the water molecules are on average closer to each other than in the liquid or gas states. At low enough temperatures, this attraction overcomes the tendency to move toward higher entropy resulting in water freezing.

However, even in these cases of locally decreasing entropy, the second law of thermodynamics is not violated, for the changes are always exothermic — heat is released. The heat leaving the local system (e.g.,  a cup of freezing water) and entering the surrounding environment increases the latter’s entropy by an amount greater than the entropy decrease of the local system. Therefore, the total entropy of the universe increases. The problem for all theories of origin of life now becomes quite evident. The simplest functional cell compared to its most basic building blocks has both lower entropy and higher energy. And, natural systems never both decrease in entropy and increase in energy at the same time. Such an event would be like rolling countless sixes in a row when the dice are strongly loaded against rolling even one. Therefore, the origin of life through purely natural processes would seem as implausible as water on a hot summer day spontaneously freezing or a river flowing unaided uphill for thousands of miles.

Physicists and chemists often combine entropy and energy (or enthalpy) together into what is called the  free energy of a system. The change of free energy is always negative for spontaneous changes  (e.g., wood burning or ice melting in summer), and it directly relates to the total increase in entropy of the universe. The challenge for the origin of life is then explaining how billions of atoms could spontaneously come together into a state of significantly higher free energy. The chance of such an event happening through thermal fluctuations was calculated by biophysicist Harold Morowitz to be less than 1 part in 10 to the power of a hundred million This number comes directly from an estimation of the free energy of life, and the free energy is a path-independent function. Therefore, this maximum probability estimate is not meaningfully dependent on the theoretical route that led to life (e.g., protein-first versus RNA world) or on the number of steps involved. The probability is always essentially zero.

At face value this thermodynamic analysis for the origin of life would seem to negate any possible materialistic solution to the problem. However, theorists have long recognized one remaining loophole. Morowitz’s calculations assumed that the system was in a state near equilibrium. For instance, some lightning bolt could have struck a pond of prebiotic chemicals at night causing atoms to come together into different configurations. The pond would then quickly settle back into a calm state where the temperature, concentrations, and other variables would remain fairly uniform. However, many argue that the origin of life took place in a system strongly driven away from equilibrium, such as a pond subjected to intense sunlight or the bottom of the ocean near a hydrothermal vent flooding its surroundings with superheated water and high-energy chemicals. Such settings are commonly referred to as non-equilibrium dissipative systems. Their common characteristic is that classical thermodynamics breaks down, so the previous analyses do not completely hold. Instead, principles of non-equilibrium thermodynamics must be applied, which are far more complex and less well understood. Moreover, the energy from these outside sources is hoped to enable the free-energy barrier to be overcome.

However, such appeals to non-equilibrium systems do little to solve the basic thermodynamic problems. First, no system could be maintained far from equilibrium for more than a limited amount of time. The sun is only out during the day, and superheated water at the bottom of the ocean would eventually migrate away from any hydrothermal vents. Any progress made toward forming a cell would be lost as the system reverted toward equilibrium (lower free energy) and thus away from any state approaching life. Second, the input of raw solar, thermal, or other forms of energy actually  increase the entropy of the system, thus moving it in the wrong direction. For instance, the  ultraviolet light from the sun or heat from  hydrothermal vents  would less easily form the complex chemical structures needed for life than break them apart. Finally, in non-equilibrium systems the differences in temperature, concentrations, and other variables act as thermodynamic forces which drive heat transfer, diffusion, and other thermodynamic flows. These flows create  microscopic sources of entropy production, again moving the system away from any reduced-entropy state associated with life. In short, the processes occurring in non-equilibrium systems, as in their near-equilibrium counterparts, generally do the opposite of what is actually needed.