Twenty years later and proto-life is more irreducibly complex than ever

Galloping Flagella and Cilia Railroads -- Getting Ready to Celebrate Twenty Years of Darwin's Black Box

Evolution News & Views 

ary of the publication of Darwin's Black Box (it appeared on August 2, 1996, to be precise). Michael Behe's book inspired a generation of Darwin discontents and showed that intelligent design was (and still is) firmly based on cutting-edge science. Among other highlights, he showcased two cellular organelles to illustrate his concept of irreducible complexity: the cilium and the flagellum. 

These organelles, protruding from the cell into the environment, could not be built by a Darwinian mechanism, he argued, because they are composed of multiple, independent parts required for function. Like a mousetrap, they could not work unless all the parts were present together at the same time.

All true, but in the intervening years molecular biologists have learned a great deal more about cilia and flagella. The revelations keep coming, like down to the day before yesterday.

Galloping Cilia

In fascinating news from the University of Cambridge, we learn that "Algae use their 'tails' to gallop and trot like quadrupeds." (Those tails are Behe's famous flagella, though differing in structure from the bacterial flagella.) You can see for yourself in the embedded videos that single-celled algae named Chlamydomonas use their flagella in coordinated ways "to achieve a remarkable diversity of swimming gaits."

When it comes to four-legged animals such as cats, horses and deer, or even humans, the concept of a gait is familiar, but what about unicellular green algae with multiple limb-like flagella? The latest discovery, published in the journal Proceedings of the National Academy of Sciences, shows that despite their simplicity, microalgae can coordinate their flagella into leaping, trotting or galloping gaits just as well.[Emphasis added.]

They trot. They gallop. They leap in a manner similar to the "pronk" of a springbok, where the animal arches its back and springs all four feet off the ground together. The resemblance is uncanny, despite a difference in size of many orders of magnitude. The cells even know two different galloping gaits: a rotary gait and a transverse gait. How is this possible for single-celled organisms lacking neurons?

In vertebrates, gaits are controlled by central pattern generators, which can be thought of as networks of neural oscillators that coordinate output. Depending on the interaction between these oscillators, specific rhythms are produced, which, mathematically speaking, exhibit certain spatiotemporal symmetries. In other words, the gait doesn't change when one leg is swapped with another -- perhaps at a different point in time, say a quarter-cycle or half-cycle later.

It turns out the same symmetries also characterise the swimming gaits of microalgae, which are far too simple to have neurons. For instance, microalgae with four flagella in various possible configurations can trot, pronk or gallop, depending on the species.

Dr. Kirsty Wan was amazed when she first observed this, saying, "I realised immediately that this behaviour could only be due to something inside the cell rather than passive hydrodynamics." Think of how this expands the argument for irreducible complexity:

The researchers determined that it is in fact the networks of elastic fibres which connect the flagella deep within the cell that coordinate these diverse gaits. In the simplest case of Chlamydomonas, which swims a breaststroke with two flagella, absence of a particular fibre between the flagella leads to uncoordinated beating. Furthermore, deliberately preventing the beating of one flagellum in an alga with four flagella has zero effect on the sequence of beating in the remainder.

Dr. Behe will be pleased to see this additional level of design. "The findings also raise intriguing questions about the evolution of the control of peripheral appendages, which must have arisen in the first instance in these primitive microorganisms," one of the paper's authors comments. Surely the first question should be, "Did it evolve at all?"

Two-Lane Highways in the Cilium

Any freshman confronted with an electron micrograph of a cilium must be impressed by the beautiful symmetry of its 9x2 structure (see the figure in Behe, p. 60). The elements of the structure are microtubules: long filaments that look like white dots in cross section. They are arranged in pairs around the periphery. The question is, "Why"? Until now, scientists were not sure. Science Magazine has just now come out with the answer: "Microtubule doublets are double-track railways for intraflagellar transport trains." One microtubule is for going up; the other is for coming down!

Cilia contain a well-ordered array of microtubule doublets along their length. A longstanding question in cilium structure and function is why the microtubule arrangement in cilia is so complex. Stepanek and Pigino developed a time-resolved correlative fluorescence and three-dimensional electron microscopy method to show that the doublets provide directionality to intraflagellar transport. One microtubule in the pair moves cargoes up to the ciliary tip. Meanwhile, the other microtubule moves cargoes back to the cell body. These results explain why the axoneme is built out of microtubule doublets and suggest a mechanistic picture of how the logistics of bidirectional intraflagellar transport are regulated.

What's really interesting about the paper is the constant use of railroad terminology. There are "cargo trains" with "motors" that ride on microtubule "tracks" for "transportation." They function as "railways for intraflagellar transport" (IFT). Nowhere is a discussion of evolution to be found. Maybe that's because everyone knows train transportation systems are intelligently designed.

Ludek Stepanek and Gaia Pigino from the Max Planck Institute observed the trains going up and down, but never colliding. They wondered how the trains avoid collisions; do they swing around each other, like using a passing lane? No; it turns out that they each have dedicated lanes.

Moreover, the upward-moving (anterograde) cargo trains use kinesin-II motors, the downward-moving cargo trains use dynein motors. How does each one know the lane to use, since the microtubules are made of the same track material? It appears there may be post-translational modifications of the track proteins (tubulins) that allow the engines to recognize the right lane to use. The situation gets even more complex from there:

This might contribute to the efficiency of IFT by providing optimized tracks for kinesin and dynein motors in addition to the IFT train segregation. Nevertheless, the effect of such modifications on the control of IFT in vivo remains unclear. Alternatively, a specific molecular machinery to direct trains to the correct microtubule could be present at the base and tip of the axoneme. More complex motor regulation could be necessary in the sensory cilia of Caenorhabditis elegans, where the B-microtubules do not extend beyond the middle segment of the flagellum. There, the kinesin-II moves only in the middle segment, and an additional motor, OSM-3, is required to bring cargo to the tip along the A-microtubules. Regardless of the mechanisms involved in the recognition of the microtubules by the motors, our work highlights the critical role played by microtubule doublets in the assembly of cilia.

Cilia are present on most eukaryotic cells and are involved in many essential functions, such as clearing the throat of debris (in which they wave in coordinated sweeping motions), and sensing the environment like antennae. Defects in cilium construction cause debilitating diseases or death, underscoring Behe's concept of irreducible complexity.

It's satisfying to report these new discoveries about cilia and flagella, confirming, as they do, Behe's original insights. The case for intelligent design gets stronger all the time.

Putting the Darwinian debate in its place.

David Berlinski: Does Darwin Matter?

David Berlinski

you write about affect the way we live? Why should the Darwin question matter to people who don't normally concern themselves with scientific theories?

DB: I think of the Darwinian debate in the way that Dickens thought of Jardynce v Jarndyce in Bleak House. It is awfully easy to be sucked into it, and once suckered, awfully difficult to get out. I have seen it so often. A man wakes and because has read a book or scanned an essay, he is persuaded that he can make a contribution. He is eager to make it. He offers his opinion on the Internet and is gratified by the prospect of the congratulations that he is shortly to receive. No one pays the slightest attention. He then discovers that to be heard, it is necessary that he amplifies his level of abuse. He does that, referring to the Discovery Institute as the Dishonesty Institute. Repeating the phrase as he moves his bowels affords him an unexpected pleasure. As his influence remains insignificant, his indignation mounts. In the morning, he scuttles to his computer to check his own postings; satisfied when he finds them, and beside himself when he fails. His appetite for conflict sharpens. He becomes determined to exaggerate every issue; and to magnify trivialities. Sooner or later, his Internet presence seems real, and his real life unreal. He ends in the state achieved by almost every Internet blogger: He commences to gibber repetitively. Glen Davidson, who posts to David Klinghoffer's blog, has recently entered the gibbering state.

It is all very sad. I have warned about the phenomenon many times.

Does Darwin matter? Yes, of course it matters. It matters a great deal. It matters whether the theory is true because for better or worse we value the truth and struggle to find it; but it would matter far more were we able to say once and for all that the theory is false. Darwinism involves a way of thought in biology, and were it to go, it would take a great many assumptions along with it. Just think of vitalism, for example. To say a word in its favor is at once to be accused of the cheapest kind of intellectual sentimentality. We know better and if we do not know better, theydo. But hold on, please do. If by vitalism one means something like the 19th century idea of a vital fluid that informs living systems, then I am with them. That is so much sentimentality. But if by vitalism one means the thesis that living systems cannot be completely explained in terms of their physics or their chemistry -- what then? Something must explain the difference, no? And if it is not a fluid, as naïve 19th-century biologists sometimes thought, it does not follow that it is nothing.

Nothing in biology makes sense except in the light of evolution.

This remark is half right: Nothing in biology does make sense. It is for the biology of the future to start making sense of it. If that in the end involves religious ideas or even religious I, that's fine with me. Let's ask the questions first, and reject the wrong answers when we know that they are wrong.

Pakistan:a country with an army or an army with a country?:Pros and Cons.

Leviathan vs.Darwin

Crocodile eyes are fine-tuned for lurking
By Jonathan Webb

A new study reveals how crocodiles' eyes are fine-tuned for lurking at the water surface to watch for prey.
The "fovea", a patch of tightly packed receptors that delivers sharp vision, forms a horizontal streak instead of the usual circular spot.
This allows the animal to scan the shoreline without moving its head, according to Australian researchers.
They also found differences in the cone cells, which sense colours, between saltwater and freshwater crocs.
Published in the Journal of Experimental Biology, the findings suggest that although the beasts have very blurry vision underwater, they do use their eyes beneath the surface.

This is because light conditions are different in salt and freshwater habitats, but only underwater - and the crocodiles' eyes show corresponding tweaks.
"There's generally more blue light in saltwater environments, and more red light in freshwater environments. Animals tend to adapt to this," explained Nicolas Nagloo, a PhD student at the University of Western Australia.
He and his colleagues studied eyeballs from juvenile "salties" and "freshies", shipped to the university from a crocodile farm in Broome.
When they measured the light absorbed by single photoreceptors in the retina, they found that those of the freshwater crocs were shifted towards longer, redder wavelengths compared with their saltwater cousins.

Finding this skewed sensitivity in crocodiles was unexpected, Mr Nagloo said, because the famous predators were only semi-aquatic and did their hunting, feeding and mating on land."It's surprising because these guys can't actually focus underwater. [But] light sensitivity seems to be important to them," he told BBC News.
"That tells us there's potentially some aspect of their behaviour underwater that we're not aware of yet."
The team also studied the density of receptors across the crocodile retina. In this regard, the two species were more similar.
Overall, crocodile vision appears to be less precise than ours, achieving a clarity some six or seven times lower than the human eye. But their "foveal streak" is a striking adaptation that suits their lifestyle perfectly.
The fovea is a dent in the retina, containing a huge concentration of receptor cells. The indentation arises because other cells, which transmit visual information to the brain, are shifted to the sides."Typically, the fovea is circular and located in the centre of the retina. It provides animals with an area of very high visual clarity, in a small area of their visual environment," Mr Nagloo said.
It is this small patch of high-resolution information that allows us, for example, to read; but we humans have to move our eyes around to drink in details across a scene.
"In the case of crocodiles... it's spread across the middle of the retina, and it gives them maximum clarity all along the visual horizon."
This arrangement reflects the predator's iconic ability to lurk with just its eyes above the water, waiting motionless for prey to wander too close to the river's edge.Other animals, particularly mammals like deer and rabbits that live in open spaces and themselves face predation, are known to possess a similar "visual streak". But that is a more subtle feature than the furrow-shaped fovea of the crocodile, Mr Nagloo said.
"A visual streak is just an elevated cell density, in an elongated shape. A fovea takes that to the extreme - the number of photoreceptors is so high that they have to move the transmitters away, to make room for them. So the wiring is different.
"I haven't seen any other animals with this kind of specialisation."

Darwinism and S.D.L algorithm II

How Did Birds Get Their Wings? Bacteria May Provide a Clue to the Genomic Basis of Evolutionary Innovation, Say Evolutionists

That evolution occurred is known to be a fact but how evolution occurred is not known. In particular we are ignorant of how evolutionary innovations arose. Of course biological novelties and innovations arose from a series of random chance events, but it is less than reassuring that we cannot provide more detail. How exactly did the most complex designs spontaneously arise? What mechanisms overcame, over and over, the astronomical entropy barriers, by sheer luck of the draw? As Craig MacLean’s and Andreas Wagner’s, and coworker’s, new PLOS Genetics paper begins, “Novel traits play a key role in evolution, but their origins remain poorly understood.” Could it be that evolution is not actually a fact? No, not according to evolutionists. And this new paper claims to provide the basis for how the seemingly impossible became the mundane.

The paper begins by summarizing the many proposed genetic mechanisms for the evolution of biological innovations:

An evolutionary innovation is a new trait that allows organisms to exploit new ecological opportunities. Some popular examples of innovations include flight, flowers or tetrapod limbs [1,2]. Innovation has been proposed to arise through a wide variety of genetic mechanisms, including: domain shuffling [3], changes in regulation of gene expression [4], gene duplication and subsequent neofunctionalization [5,6], horizontal gene transfer [7,8] or gene fusion [9]. Although innovation is usually phenotypically conspicuous, the underlying genetic basis of innovation is often difficult to discern, because the genetic signature of evolutionary innovation erodes as populations and species diverge through time.

1. Mayr E. Animal Species and Evolution. Cambridge: MA: Harvard University Press; 1963.

2. Pigliucci M. What, if anything, is an evolutionary novelty? Philos Sci. 2008;75: 887–898. Available:http://philpapers.org/rec/PIGWIA

3. Patthy L. Genome evolution and the evolution of exon-shuffling—a review. Gene. 1999;238: 103–14. Available: http://www.ncbi.nlm.nih.gov/pubmed/10570989 pmid:10570989

4. True JR, Carroll SB. Gene co-option in physiological and morphological evolution. Annu Rev Cell Dev Biol. 2002;18: 53–80. doi: 10.1146/annurev.cellbio.18.020402.140619. pmid:12142278

5. Zhang J. Evolution by gene duplication: An update. Trends Ecol Evol. 2003;18: 292–298. doi: 10.1016/S0169-5347(03)00033-8.

6. Bergthorsson U, Andersson DI, Roth JR. Ohno’s dilemma: evolution of new genes under continuous selection. Proc Natl Acad Sci U S A. 2007;104: 17004–9. doi: 10.1073/pnas.0707158104. pmid:17942681

7. Boucher Y, Douady CJ, Papke RT, Walsh DA, Boudreau MER, Nesbø CL, et al. Lateral gene transfer and the origins of prokaryotic groups. Annu Rev Genet. 2003;37: 283–328. doi: 10.1146/annurev.genet.37.050503.084247. pmid:14616063

8. Wiedenbeck J, Cohan FM. Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol Rev. 2011;35: 957–976. doi: 10.1111/j.1574-6976.2011.00292.x. pmid:21711367

9. Thomson TM, Lozano JJ, Loukili N, Carrió R, Serras F, Cormand B, et al. Fusion of the human gene for the polyubiquitination coeffector UEV1 with Kua, a newly identified gene. Genome Res. 2000;10: 1743–56. pmid:11076860 doi: 10.1101/gr.gr-1405r

The unspoken problem here is, as usual, serendipity. The various proposed genetic mechanisms for the evolution of biological innovations all suggest an amazing bit of fortuitous luck. For random chance events just happened to create these various complicated structures and mechanisms (such as horizontal gene transfer and protein domains their shuffling) which then produced new evolutionary breakthroughs.

Evolution didn’t know what was coming. Evolution did not plan this out, it did not realize that horizontal gene transfer would lead the way to new biological worlds. The evolution of horizontal gene transfer would require a long sequence of random mutations, many of which would not provide any fitness advantage. And when the construction project was completed, and the first horizontal gene transfer capability was possible, there would be no immediate advantage.

This is because there would have been no genes to transfer. The mechanism works only when it is present in more than one, neighboring, cells. One cell gives, and another cells receives. By definition the mechanism involves multiple cells.

But it doesn’t stop there. Even if the first horizontal gene transfer capability was able to spread across a population, and even if it did provide a fitness advantage to the fortunate citizens, there would not be even a hint of the enormous world of biological innovations that had just been opened.

In other words, what this evolutionary narrative entails is monumental serendipity. Biological structures and mechanisms (horizontal gene transfer in this case, but it is the same story with the other hypotheses listed above) are supposed to have evolved as a consequence of a local, proximate, fitness advantage: a bacteria could now have a gene it didn’t have before.

But it just so happened that the new structures and mechanisms would also, as a free bonus, be just what was needed to produce all manner of biological innovations, far beyond assisting a lowly bacteria increase its fecundity.

This is monumental serendipity.

The science contradicts the theory

Undaunted, the new paper finds that one of the other mechanisms, gene duplication and subsequent neofunctionalization, is a key enabler and pathway to biological innovations.

That conclusion resulted from what otherwise was a fine piece of research work. The experimenters exposed different populations of Pseudomonas aeruginosa, a dangerous infectious bacteria, to 95 new sources of its favorite food: carbon.

The bacteria had to adjust to the new flavors of carbon and they did so with various genetic modifications, including various genetic mutations. In the most challenging cases (where the new carbon sources were most difficult for the bacteria to adjust to), the bacteria often produced mutations in genes involved in transcription and metabolism. And these mutations often occurred in genes where there were multiple copies, so the mutations occurred in one copy while the other copy could continue in its normal duties.

The problem is, these genetic duplicates were preexisting in the P. aeruginosa genome. This is yet another instance of serendipity.

Why? Because preexisting duplicates are not common. Only about 10% of the genes have duplicates lying around, and fortunately, the genes needed for adaptation (involving transcription and metabolism) just happened to have such duplicates.

Now there were a few instances of de novo gene duplication. That is, once the experiment began, and after the P. aeruginosa populations were exposed to the challenging diets, a total of six genes underwent duplication events. But in each and every case, the duplication events occurred repeatedly and independently, in different populations (for each of the 95 different carbon sources, the experimenters ran four parallel trials with independent populations).

This result indicates directed gene duplication. This is because it is highly unlikely that random, chance, gene duplication events just happened hit on the same gene in different populations. Here is an example calculation.

Let’s assume that in the course of the experiment, which ran for 30 days and about 140 generations of P. aeruginosa, some genes may undergo duplication events by chance. Next assume there is a particular gene that needs to be duplicated and modified in order to for P. aeruginosa to adapt to the new food source. (Note that there may be several such genes, but as we shall see that will not affect the conclusion). Given that there are four separate, independent trials, what is the probability that the gene will be duplicated in two or more of those trials?

Let P_dup be the probability that any gene is duplicated in the course of the experiment. For our gene of interest, it may be duplicated in 0, 1, 2, 3, or all 4 of the trials. The binomial distribution describes the probability, P, of each of these outcomes. To answer our question (i.e., What is the probability that the gene will be duplicated in two or more of those trials?) we sum the binomial distribution’s value for N = 2, 3 and 4. In other words, we calculate P(2) + P(3) + P(4).

This will give us the probability of observing what was observed in the experiment (i.e., the duplication events occurred repeatedly and independently, in different populations, in all 6 cases where duplication events were observed).

Well for a reasonable value of P_dup, the probability that any gene is duplicated in the course of the experiment, such as 0.0001, the probability of observing multiple duplications events for any given food source (i.e., P(2) + P(3) + P(4)) is about 60 in one billion, or 6  times 10^-8. Even worse, the probability of observing this in all 6 cases where duplication events were observed is about 5 times 10^-44.

It isn’t going to happen.

Exceptionally high rates of gene duplication, in particular genomic regions of Salmonella typhimurium, in a high growth rate medium, were observed to be about 0.001 and even slightly above 0.01 in rare cases.

If we go all out and set P_dup to an unrealistically high 0.1, our results are still unlikely. The P(2) + P(3) + P(4)) is .05, and the probability of observing this in all 6 cases where duplication events were observed is about 2 times 10^-8.

In order to raise these probabilities to reasonable levels, such that what was observed in the experiment is actually likely to have occurred, we need to raise P_dup to much higher values. For example, for a P_dup of .67 (two-thirds probability), P(2) + P(3) + P(4)) is .89, and the probability of observing this in all 6 cases where duplication events were observed is about .5.

But even this doesn’t work. For if we were to imagine unrealistically high P_dup values of 0.1 or higher, then massive numbers of duplication events would have been observed in the experiments.

But they weren’t.

Once again, the science contradicts the theory. Our a priori assumption that evolution is a fact, and that the P. aeruginosa adaptations to the new food sources were driven by random mutations, did not work. The theory led to astronomically low probabilities of the observed results.

What the observed gene duplications are consistent with is directed gene duplications. Just as mutations have been found to be directed in cases of environmental challenges, it appears that gene duplications may also be directed.

The paper’s premise, that biological innovations such as flowers and wings are analogous to bacteria adapting to new nutrient sources, is fallacious. But setting that aside, the experimental results do not make sense on evolution’s mechanism of random mutations and natural selection. Instead, the results indicate directed adaptation.

Posted by Cornelius Hunter 

File under "well said" XXIV

“Wise men speak because they have something to say; fools because they have to say something.”
 Plato.

Design by chance and necessity S.T.O.M.Ped

Atheist biologist makes an excellent case for Intelligent Design
November 19, 2015 Posted by vjtorley under Intelligent Design


Matthew Cobb is a professor of zoology at the University of Manchester and a regular contributor over at Why Evolution Is True. Recently, while critiquing a cartoon from xkcd (shown above), he argued that our DNA is the mindless product of a series of historical accidents. But then he let the cat out of the bag, at the end of his post:

On a final note, in some cases, within this amazing noise, there are also astonishing examples of complexity which do indeed appear to be the result of optimisation – and they would boggle the mind of anyone, not just a cocky computer scientist in a hat. In Drosophila there is a gene called Dscam, which is involved in neuronal development and has four clusters of exons (bits of the gene that are expressed – hence exon – in contrast to the apparently inert introns).

Each of these exons can be read by the cell in twelve, forty-eight, thirty-three or two alternative ways. As a result, the single stretch of DNA that we call Dscam can encode 38,016 different proteins. (For the moment, this is the record number of alternative proteins produced by a single gene. I suspect there are many even more extreme examples.)

Cobb triumphantly concluded:

In other words, DNA is even more complicated than [xkcd cartoonist] Randall [Munroe] imagines – it is historical, messy, undesigned. And when occasionally it is optimised, the degree of complexity is mind-boggling. Biology is not quite impossible, it is just incredibly difficult!

But the damage was done. Even as he chided cartoonist Randall Munroe for claiming that DNA is subject to “the most aggressive optimisation process in the universe” and insisted that our genes are “a horrible, historical mess” consisting mostly of junk DNA, and that they are really the product of mindless tinkering rather than design, Cobb was forced to concede that amidst all this chaos, there were indeed some “astonishing examples of complexity which do indeed appear to be the result of optimisation” which “would boggle the mind of anyone, not just a cocky computer scientist in a hat.”

Intelligent Design supporters are often accused of appealing to something called an API: an Argument from Personal Incredulity. The acronym comes from Professor Richard Dawkins. The reasoning is supposed to go like this: I cannot imagine how complex structure X could have come about as a result of blind natural processes; therefore an intelligent being must have created it. This, Dawkins rightly points out, is not a rational argument. Certainly it has no place in a science classroom.

But my own conversion to Intelligent Design was not based on an API, but on something which I have decided to call the STOMPS Principle. STOMPS is an acronym for: Smarter Than Our Most Promising Scientists. The reasoning goes like this: if I observe a complex system which is capable of performing a task in a manner which is more ingenious than anything our best and most promising scientists could have ever designed, then it would be rational for me to assume that the system in question was also designed. That is not to say that nothing will shake my conviction, but if you claim that an unguided natural process could have done the job, then I am going to demand that you explain how the process in question could have accomplished this stupendous feat. I shall demand a specification of a mechanism, and a demonstration that this mechanism is at least capable of generating the complex system we are talking about, within the time available, without appealing to mathematical miracles (like winning the Powerball Jackpot ten times in a row). To demand any less would be the height of irrationality.

Professor Matthew Cobb concedes that our junky DNA contains genes which encode for proteins. He concedes that within the “noise” of our junky DNA, there are also “astonishing examples of complexity which do indeed appear to be the result of optimisation,” and that the complexity of this DNA code would “boggle the mind” of even “a cocky computer scientist in a hat.” This sounds like a perfect example of a case where the STOMPS Principle could be legitimately invoked. If Nature contains systems which accomplish a feat in a manner which is far better than what our best scientists can do, then it’s reasonable to infer that these systems were intelligently designed.

At this point, some evolutionists may respond by invoking what philosopher Daniel Dennett has termed Leslie Orgel’s second law: “Evolution is cleverer than you are.” The relevant question here is: cleverer at what? We have seen that all living things employ a genetic code: a set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells. Despite diligent inquiry on our part, we have yet to uncover a single instance in Nature of unguided processes generating a code of any sort – let alone one which would “boggle the mind” of even “a cocky computer scientist in a hat.” Whatever else evolution might be clever at, code-making is hardly its forte.

But, we shall be told, evolution refines the code in our DNA all the time – through natural selection winnowing random mutations, as well as purely chance-driven processes such as genetic drift. Who are we to say that it could not have generated this code by an incremental series of refinements, over billions of years?

I used to be a computer programmer, for ten years. I think I know what it means to refine computer code. Evolution doesn’t do anything like that: what it does is corrupt the code in organisms’ cells, in ways that occasionally turn out to improve those organisms’ prospects for survival. That might be good for the organisms, but from a code-bound perspective, it isn’t “good” at all: it’s just the corruption of a code. And corruption is the opposite of generation.

So when I hear someone tell me that “nature, heartless, witless nature” could have not only generated a code, but generated one which even our brightest scientists are in awe of, my response is: “You’re pulling my leg.”

Finally, I’d like to address Professor Matthew Cobb’s argument that “[o]ur genes are not perfectly adapted and beautifully designed,” because our DNA is littered with junk: they are instead the product of “evolution and natural selection.” My response to that argument is: so what? Even if Professor Cobb is right about junk DNA – and I’m inclined to think he is (for reasons I’ll discuss in another post) – that’s beside the point. At most, it shows is that DNA which doesn’t code for anything wasn’t designed. But my question is: what about the DNA which does code for proteins, and which does so in a manner that boggles the ingenuity of our brightest minds? Professor Cobb, it seems, is missing the wood for the trees here.

Junk DNA might be described as degenerate code – but there has to be a code in the first place, before it can degenerate. The existence of junk DNA cannot be used as an argument against design: all it establishes is that the designer of our DNA – whether out of benign neglect, laziness, illness, or ignorance that something has gone amiss – doesn’t always fix the code he created, when it becomes corrupted. Accordingly, junk DNA cannot be used as a legitimate argument against the proposition that the DNA in our cells which codes for genes was designed.

A personal story

A few years ago, I came across an article by an Australian botanist (who is also a creationist) named Alex Williams, entitled, “Astonishing Complexity of DNA Demolishes Neo-Darwinism” (Journal of Creation, 21(3), 2007). At the time I knew very little about specified complexity and other terms in the Intelligent Design lexicon. I heartily dislike jargon, and I was having difficulty deciding whether there was any real scientific merit to the Intelligent Design movement’s claim that certain biological systems must have been designed. But when I read Alex Williams’ article, the case for Intelligent Design finally made sense to me. What impressed me most, with my background in computer science, was that the coding in the cell was far, far more efficient than anything that our best scientists could have come up with. Here are some excerpts from the article:

The traditional understanding of DNA has recently been transformed beyond recognition. DNA does not, as we thought, carry a linear, one-dimensional, one-way, sequential code—like the lines of letters and words on this page… DNA information is overlapping-multi-layered and multi-dimensional; it reads both backwards and forwards… No human engineer has ever even imagined, let alone designed an information storage device anything like it…

There is no ‘beads on a string’ linear arrangement of genes, but rather an interleaved structure of overlapping segments, with typically five, seven or more transcripts coming from just one segment of code.
Not just one strand, but both strands (sense and antisense) of the DNA are fully transcribed.
Transcription proceeds not just one way but both backwards and forwards…
There is not just one transcription triggering (switching) system for each region, but many.
(Bold emphasis mine – VJT.)

I’d like to make it clear that as someone who believes in a 13.8 billion-year-old universe and in common descent, I do not share Williams’ creationist views. In particular, I think his argument for a young cosmos, based on Haldane’s dilemma, rests on faulty premises. But I do think that Williams is on solid scientific ground when he writes that no human engineer has ever even imagined, let alone designed an information storage device anything like DNA. Here we have an appeal to the STOMPS principle: DNA encodes information in a way which is far cleverer than anything that our most intelligent programmers could have designed, so it is reasonable to infer that DNA itself was designed by a superhuman intelligent agent.

I’d like to conclude this post with a quote from someone whose impartiality is not in doubt: Bill Gates, the founder of Microsoft Corporation, who is also an agnostic:

Biological information is the most important information we can discover, because over the next several decades it will revolutionize medicine. Human DNA is like a computer program but far, far more advanced than any software ever created. 
(The Road Ahead, Penguin: London, Revised Edition, 1996 p. 228.)

If an agnostic like Bill Gates, who is an acknowledged expert on computing, thinks that the complexity of human DNA surpasses that of any human software design, then it is surely reasonable to infer that human DNA – or at the very least, its four-billion-year-old progenitor, the DNA in the first living cell, was originally designed by some superhuman Intelligence.

Professor Cobb is undercut by one of his own commenters

We have seen that Professor Matthew Cobb’s argument against DNA having been designed is a philosophically flawed one. But reading through the comments attached to his post, I came across two comments by a reader named Eric (see here and here) which blew Professor Cobb’s case right out of the water, from a computing perspective:

… Matthew’s comment “Our genes are not perfectly adapted and beautifully designed. They are a horrible, historical mess” makes the analogy to human programming better, not worse….

I would guess that the entire etymology of computer programming languages is a result of historical contingency (i.e. a horrible, historical mess) as much as it is a result of optimization or rational choice. The reason Java forms the basis of so many internet-based languages is because that’s what was included in the earliest version of Netscape Navigator, which captured the market at the time. And the reason there are so many Visual Basic type programming languages is because Basic is what ran on the first generation of IBM personal computers. Geez, I know labs that were programming their nuclear physics detector setups in Fortran in the 1990s, and that is a language invented for use with punch cards.

Now computer programming languages will probably always require a more formal and rigorous syntax than natural language, but IMO the specific formal syntaxes that we used today are more due to the vagaries of human history than they are any sort of rational choice of the best options.

For that matter, why the frak do we even bother with www? Http vs. Https? That’s four redundant and therefore worthless letters out of five, the equivalent of 80% “junk DNA” in one of the most common and most recent human-built computer syntaxes. What sense does it make? None. Why do we have it? History.

The watchtower society's commentary on the family Of Jehovah.

SON(S) OF GOD

The expression “Son of God” primarily identifies Christ Jesus. Others referred to as “son(s) of God” include intelligent spirit creatures produced by God, the man Adam before he sinned, and humans with whom God has dealt on the basis of covenant relationship.

“Sons of the True God.” The first mention of “sons of the true God” is at Genesis 6:2-4. There such sons are spoken of as ‘beginning to notice the daughters of men, that they were good-looking; and they went taking wives for themselves, namely, all whom they chose,’ this prior to the global Flood.

Many commentators hold that these ‘sons of God’ were themselves human, being in reality men of the line of Seth. They base their argument on the fact that Seth’s line was that through which godly Noah came, whereas the other lines from Adam, that of Cain and those of any other sons born to Adam (Ge 5:3, 4), were destroyed at the Flood. So, they say that the taking as wives “the daughters of men” by “the sons of the true God” means that Sethites began to marry into the line of wicked Cain.

There is, however, nothing to show that God made any such distinction between family lines at this point. Corroborating Scriptural evidence is lacking to support the view that intermarriage between the lines of Seth and Cain is what is here meant, or that such marriages were responsible for the birth of “mighty ones” as mentioned in Ge 6 verse 4. It is true that the expression “sons of men [or “of mankind”]” (which those favoring the earlier mentioned view would contrast with the expression ‘sons of God’) is frequently used in an unfavorable sense, but this is not consistently so.—Compare Ps 4:2; 57:4; Pr 8:22, 30, 31; Jer 32:18, 19; Da 10:16.

Angelic sons of God. On the other hand, there is an explanation that finds corroborating evidence in the Scriptures. The expression “sons of the true God” next occurs at Job 1:6, and here the reference is obviously to spirit sons of God assembled in God’s presence, among whom Satan, who had been “roving about in the earth,” also appeared. (Job 1:7; see also 2:1, 2.) Again at Job 38:4-7 “the sons of God” who ‘shouted in applause’ when God ‘laid the cornerstone’ of the earth clearly were angelic sons and not humans descended from Adam (as yet not even created). So, too, at Psalm 89:6 “the sons of God” are definitely heavenly creatures, not earthlings.—See GOD (Hebrew Terms).

The identification of “the sons of the true God” at Genesis 6:2-4 with angelic creatures is objected to by those holding the previously mentioned view because they say the context relates entirely to human wickedness. This objection is not valid, however, since the wrongful interjection of spirit creatures in human affairs most certainly could contribute to or accelerate the growth of human wickedness. Wicked spirit creatures during Jesus’ time on earth, though not then materializing in visible form, were responsible for wrong human conduct of an extreme nature. (See DEMON; DEMON POSSESSION.) The mention of a mixing into human affairs by angelic sons of God could reasonably appear in the Genesis account precisely because of its explaining to a considerable degree the gravity of the situation that had developed on earth prior to the Flood.

Supporting this are the apostle Peter’s references to “the spirits in prison, who had once been disobedient when the patience of God was waiting in Noah’s days” (1Pe 3:19, 20), and to “the angels that sinned,” mentioned in connection with the “ancient world” of Noah’s time (2Pe 2:4, 5), as well as Jude’s statement concerning “the angels that did not keep their original position but forsook their own proper dwelling place.” (Jude 6) If it is denied that “the sons of the true God” of Genesis 6:2-4 were spirit creatures, then these statements by the Christian writers become enigmatic, with nothing to explain the manner in which this angelic disobedience took place, or its actual relation to Noah’s time.

Angels definitely did materialize human bodies on occasion, even eating and drinking with men. (Ge 18:1-22; 19:1-3) Jesus’ statement concerning resurrected men and women not marrying or being given in marriage but being like the “angels in heaven” shows that marriages between such heavenly creatures do not exist, no male and female distinction being indicated among them. (Mt 22:30) But this does not say that such angelic creatures could not materialize human forms and enter marriage relations with human women. It should be noted that Jude’s reference to angels as not keeping their original position and to them as forsaking their “proper dwelling place” (certainly here referring to an abandoning of the spirit realm) is immediately followed by the statement: “So too Sodom and Gomorrah and the cities about them, after they in the same manner as the foregoing ones had committed fornication excessively and gone out after flesh for unnatural use, are placed before us as a warning example.” (Jude 6, 7) Thus, the combined weight of the Scriptural evidence points to angelic deviation, the performance of acts contrary to their spirit nature, occurring in the days of Noah. There seems to be no valid reason, then, for doubting that the ‘sons of God’ of Genesis 6:2-4 were angelic sons.—See NEPHILIM.

First Human Son and His Descendants. Adam was the first human “son of God” by virtue of his creation by God. (Ge 2:7; Lu 3:38) When he was condemned to death as a willful sinner and was evicted from God’s sanctuary in Eden, he was, in effect, disowned by God and lost his filial relationship with his heavenly Father.—Ge 3:17-24.

Those descended from him have been born with inherited sinful tendencies. (See SIN, I.) Since they were born of one rejected by God, Adam’s descendants could not claim the relationship of being a son of God simply on the basis of birth. This is demonstrated by the apostle John’s words at John 1:12, 13. He shows that those who received Christ Jesus, exercising faith in his name, were given “authority to become God’s children, . . . [being] born, not from blood or from a fleshly will or from man’s will, but from God.” Sonship in relation to God, therefore, is not viewed as something automatically received by all of Adam’s descendants at birth. This and other texts show that, since Adam’s fall into sin, it has required some special recognition by God for men to be designated as his “sons.” This is illustrated in his dealings with Israel.

“Israel Is My Son.” To Pharaoh, who considered himself a god and a son of the Egyptian god Ra, Jehovah spoke of Israel as “my son, my firstborn,” and called on the Egyptian ruler to “send my son away that he may serve me.” (Ex 4:22, 23) Thus the entire nation of Israel was viewed by God as his “son” because of being his chosen people, a “special property, out of all the peoples.” (De 14:1, 2) Not only because Jehovah is the Source of all life but more specifically because God had, in harmony with the Abrahamic covenant, produced this people, he is called their “Creator,” their “Former,” and their “Father,” the one by whose name they were called. (Compare Ps 95:6, 7; 100:3; Isa 43:1-7, 15; 45:11, 12, 18, 19; 63:16.) He had ‘helped them even from the belly,’ evidently referring to the very beginning of their development as a people, and he ‘formed’ them by his dealings with them and by the Law covenant, giving shape to the national characteristics and structure. (Isa 44:1, 2, 21; compare God’s expressions to Jerusalem at Eze 16:1-14; also Paul’s expressions at Ga 4:19 and 1Th 2:11, 12.) Jehovah protected, carried, corrected, and provided for them as a father would for his son. (De 1:30, 31; 8:5-9; compare Isa 49:14, 15.) As “a son,” the nation should have served to the praise of its Father. (Isa 43:21; Mal 1:6) Otherwise Israel would belie its sonship (De 32:4-6, 18-20; Isa 1:2, 3; 30:1, 2, 9), even as some of the Israelites acted in disreputable ways and were called “sons of belial” (literal Hebrew expression rendered “good-for-nothing men” at De 13:13 and other texts; compare 2Co 6:15). They became “renegade sons.”—Jer 3:14, 22; compare 4:22.

It was in this national sense, and due to their covenant relationship, that God dealt with the Israelites as sons. This is seen by the fact that God simultaneously refers to himself not only as their “Maker” but also as their “Repurchaser” and even as their “husbandly owner,” this latter expression placing Israel in the relationship of a wife to him. (Isa 54:5, 6; compare Isa 63:8; Jer 3:14.) It was evidently with their covenant relationship in mind, and recognizing God as responsible for the formation of the nation, that the Israelites addressed themselves to Jehovah as “our Father.”—Isa 63:16-19; compare Jer 3:18-20; Ho 1:10, 11.

The tribe of Ephraim became the most prominent tribe of the northern kingdom of ten tribes, its name often standing for that entire kingdom. Because Jehovah chose to have Ephraim receive the firstborn son’s blessing from his grandfather Jacob instead of Manasseh, the real firstborn son of Joseph, Jehovah rightly spoke of the tribe of Ephraim as “my firstborn.”—Jer 31:9, 20; Ho 11:1-8, 12; compare Ge 48:13-20.

Individual Israelite ‘sons.’ God also designated certain individuals within Israel as his ‘sons,’ in a special sense. Psalm 2, attributed to David at Acts 4:24-26, evidently applies to him initially when speaking of God’s “son.” (Ps 2:1, 2, 7-12) The psalm was later fulfilled in Christ Jesus, as the context in Acts shows. Since the context in the psalm shows that God is speaking, not to a baby, but to a grown man, in saying, “You are my son; I, today, I have become your father,” it follows that David’s entry into such sonship resulted from God’s special selection of him for the kingship and from God’s fatherly dealings with him. (Compare Ps 89:3, 19-27.) In a similar way Jehovah said of David’s son Solomon, “I myself shall become his father, and he himself will become my son.”—2Sa 7:12-14; 1Ch 22:10; 28:6.

Loss of sonship. When Jesus was on earth the Jews still claimed God as their “Father.” But Jesus bluntly told certain opposing ones that they were ‘of their father the Devil,’ for they listened to and did the will and works of God’s Adversary; hence they showed they were “not from God.” (Joh 8:41, 44, 47) This again shows that sonship with God on the part of any of Adam’s descendants requires not simply some natural fleshly descent but primarily God’s provision of a spiritual relationship with Him, and that such relationship, in turn, requires that the “sons” keep faith with God by manifesting his qualities, being obedient to his will, and faithfully serving his purpose and interests.

Christian Sons of God. As John 1:11, 12 makes evident, only some of the nation of Israel, those showing faith in Christ Jesus, were granted “authority to become God’s children.” Christ’s ransom sacrifice brought this Jewish “remnant” (Ro 9:27; 11:5) out from under the Law covenant, which, though good and perfect, nevertheless condemned them as sinners, as slaves in the custody of sin; Christ thus freed them that they might “receive the adoption as sons” and become heirs through God.—Ga 4:1-7; compare Ga 3:19-26.

People of the nations, previously “without God in the world” (Eph 2:12), also became reconciled to God through faith in Christ and came into the relationship of sons.—Ro 9:8, 25, 26; Ga 3:26-29.

As did Israel, these Christians form a covenant people, being brought into the “new covenant” made valid by the application of Christ’s shed blood. (Lu 22:20; Heb 9:15) However, God deals individually with Christians in accepting them into this covenant. Because they hear the good news and exercise faith, they are called to be joint heirs with God’s Son (Ro 8:17; Heb 3:1), are “declared righteous” by God on the basis of their faith in the ransom (Ro 5:1, 2), and thus are ‘brought forth by the word of truth’ (Jas 1:18), being “born again” as baptized Christians, begotten or produced by God’s spirit as his sons, due to enjoy spirit life in the heavens (Joh 3:3; 1Pe 1:3, 4). They have received, not a spirit of slavery such as resulted from Adam’s trespass, but “a spirit of adoption as sons, by which spirit [they] cry out: ‘Abba, Father!’” the term “Abba” being an intimate and endearing form of address. (Ro 8:14-17; see ABBA; ADOPTION [A Christian significance].) Thanks to Christ’s superior mediatorship and priesthood and God’s undeserved kindness expressed through him, the sonship of these spirit-begotten Christians is a more intimate relationship with God than that enjoyed by fleshly Israel.—Heb 4:14-16; 7:19-25; 12:18-24.

Maintaining sonship. Their “new birth” to this living hope (1Pe 1:3) does not of itself guarantee their continued sonship. They must be “led by God’s spirit,” not by their sinful flesh, and they must be willing to suffer as Christ did. (Ro 8:12-14, 17) They must be “imitators of God, as beloved children” (Eph 5:1), reflecting his divine qualities of peace, love, mercy, kindness (Mt 5:9, 44, 45; Lu 6:35, 36), being “blameless and innocent” of the things characterizing the “crooked and twisted generation” among whom they live (Php 2:15), purifying themselves of unrighteous practices (1Jo 3:1-4, 9, 10), being obedient to God’s commandments, and accepting his discipline (1Jo 5:1-3; Heb 12:5-7).

Attaining full adoption as sons. Although called to be God’s children, while in the flesh they have only a “token of what is to come.” (2Co 1:22; 5:1-5; Eph 1:5, 13, 14) That is why the apostle, though speaking of himself and his fellow Christians as already “God’s sons,” could nevertheless say that “we ourselves also who have the firstfruits, namely, the spirit, yes, we ourselves groan within ourselves, while we are earnestly waiting for adoption as sons, the release from our bodies by ransom.” (Ro 8:14, 23) Thus, after conquering the world by faithfulness until death, they receive the full realization of their sonship by being resurrected as spirit sons of God and “brothers” of God’s Chief Son, Christ Jesus.—Heb 2:10-17; Re 21:7; compare Re 2:7, 11, 26, 27; 3:12, 21.

Those who are God’s spiritual children, called to this heavenly calling, know they are such, for God’s ‘spirit itself bears witness with their spirit that they are God’s children.’ (Ro 8:16) This evidently means that their spirit acted as an impelling force in their lives, moving them to respond positively to the expressions of God’s spirit through his inspired Word in speaking about such heavenly hope and also to his dealings with them by that spirit. Thus they have the assurance that they are indeed God’s spiritual children and heirs.

Glorious Freedom of the Children of God. The apostle speaks of “the glory that is going to be revealed in us” and also of “the eager expectation of the creation . . . waiting for the revealing of the sons of God.” (Ro 8:18, 19) Since the glory of these sons is heavenly, it is clear that such “revealing” of their glory must be preceded by their resurrection to heavenly life. (Compare Ro 8:23.) However, 2 Thessalonians 1:6-10 indicates that this is not all that is involved; it speaks of “the revelation of the Lord Jesus” as bringing judicial punishment on those judged adversely by God, doing so “at the time he comes to be glorified in connection with his holy ones.”—See REVELATION.

Since Paul says that “the creation” is waiting for this revealing, and will then be “set free from enslavement to corruption and have the glorious freedom of the children of God,” it is apparent that others aside from these heavenly “sons of God” receive benefit from their revelation in glory. (Ro 8:19-23) The Greek term rendered “creation” can refer to any creature, human or animal, or to creation in general. Paul refers to it here as being in “eager expectation,” as “waiting,” as “subjected to futility, [though] not by its own will,” as being “set free from enslavement to corruption [in order to] have the glorious freedom of the children of God,” and as “groaning together” even as the Christian “sons” groan within themselves; these expressions all point conclusively to the human creation, the human family, hence not to creation in general, including animals, vegetation, and other creations, both animate and inanimate. (Compare Col 1:23.) This must mean, then, that the revelation of the sons of God in glory opens the way for others of the human family to enter into a relationship of actual sonship with God and to enjoy the freedom that accompanies such relationship.—See DECLARE RIGHTEOUS (Other Righteous Ones); GREAT CROWD.

Since Christ Jesus is the one foretold to become the “Eternal Father” (Isa 9:6) and since the Christian “sons of God” become his “brothers” (Ro 8:29), it follows that there must be others of the human family who gain life through Christ Jesus and who are, not his joint heirs and associate kings and priests, but his subjects over whom he reigns.—Compare Mt 25:34-40; Heb 2:10-12; Re 5:9, 10; 7:9, 10, 14-17; 20:4-9; 21:1-4.

It may be noted also that James (1:18) speaks of these spirit-begotten “sons of God” as being “certain firstfruits” of God’s creatures, an expression similar to that used of the “hundred and forty-four thousand” who are “bought from among mankind” as described at Revelation 14:1-4. “Firstfruits” implies that other fruits follow, and hence the “creation” of Romans 8:19-22 evidently applies to such ‘after fruits’ or ‘secondary fruits’ of mankind who, through faith in Christ Jesus, gain eventual sonship in God’s universal family.

In speaking of the future “system of things” and “the resurrection from the dead” to life in that system, Jesus said that these become “God’s children by being children of the resurrection.”—Lu 20:34-36.

From all the foregoing information it can be seen that ‘sonship’ of humans in relation to God is viewed from several different aspects. In each case, then, the sonship must be viewed in context to determine what it embraces and the exact nature of the filial relationship.

Christ Jesus, the Son of God. The Gospel account by John particularly emphasizes Jesus’ prehuman existence as “the Word” and explains that “the Word became flesh and resided among us, and we had a view of his glory, a glory such as belongs to an only-begotten son from a father.” (Joh 1:1-3, 14) That his sonship did not begin with his human birth is seen from Jesus’ own statements, as when he said, “What things I have seen with my Father I speak” (Joh 8:38, 42; compare Joh 17:5, 24), as well as from other clear statements of his inspired apostles.—Ro 8:3; Ga 4:4; 1Jo 4:9-11, 14.

“Only-begotten.” Some commentators object to the translation of the Greek word mo·no·ge·nes′ by the English “only-begotten.” They point out that the latter portion of the word (ge·nes′) does not come from gen·na′o (beget) but from ge′nos (kind), hence the term refers to ‘the only one of a class or kind.’ Thus many translations speak of Jesus as the “only Son” (RS; AT; JB) rather than the “only-begotten son” of God. (Joh 1:14; 3:16, 18; 1Jo 4:9) However, while the individual components do not include the verbal sense of being born, the usage of the term definitely does embrace the idea of descent or birth, for the Greek word ge′nos means “family stock; kinsfolk; offspring; race.” It is translated “race” in 1 Peter 2:9. The Latin Vulgate by Jerome renders mo·no·ge·nes′ as unigenitus, meaning “only-begotten” or “only.” This relationship of the term to birth or descent is recognized by numerous lexicographers.

Edward Robinson’s Greek and English Lexicon of the New Testament (1885, p. 471) gives the definition of mo·no·ge·nes′ as: “only born, only begotten, i.e. an only child.” The Greek-English Lexicon of the New Testament by W. Hickie (1956, p. 123) also gives: “only begotten.” The Theological Dictionary of the New Testament, edited by G. Kittel, states: “The μονο- [mo·no-] does not denote the source but the nature of derivation. Hence μονογενής [mo·no·ge·nes′] means ‘of sole descent,’ i.e., without brothers or sisters. This gives us the sense of only-begotten. The ref. is to the only child of one’s parents, primarily in relation to them. . . . But the word can also be used more generally without ref. to derivation in the sense of ‘unique,’ ‘unparalleled,’ ‘incomparable,’ though one should not confuse the refs. to class or species and to manner.”—Translator and editor, G. Bromiley, 1969, Vol. IV, p. 738.

As to the use of the term in the Christian Greek Scriptures or “New Testament,” this latter work (pp. 739-741) says: “It means ‘only-begotten.’ . . . In [John] 3:16, 18; 1 Jn. 1Jo 4:9; [John] 1:18 the relation of Jesus is not just compared to that of an only child to its father. It is the relation of the only-begotten to the Father. . . . In Jn. Joh 1:14, 18; 3:16, 18; 1 Jn. 1Jo 4:9 μονογενής denotes more than the uniqueness or incomparability of Jesus. In all these verses He is expressly called the Son, and He is regarded as such in Joh 1:14. In Jn. μονογενής denotes the origin of Jesus. He is μονογενής as the only-begotten.”

In view of these statements and in view of the plain evidence of the Scriptures themselves, there is no reason for objecting to translations showing that Jesus is not merely God’s unique or incomparable Son but also his “only-begotten Son,” hence descended from God in the sense of being produced by God. This is confirmed by apostolic references to this Son as “the firstborn of all creation” and as “the One born [form of gen·na′o] from God” (Col 1:15; 1Jo 5:18), while Jesus himself states that he is “the beginning of the creation by God.”—Re 3:14.

Jesus is God’s “firstborn” (Col 1:15) as God’s first creation, called “the Word” in his prehuman existence. (Joh 1:1) The word “beginning” in John 1:1 cannot refer to the “beginning” of God the Creator, for he is eternal, having no beginning. (Ps 90:2) It must therefore refer to the beginning of creation, when the Word was brought forth by God as his firstborn Son. The term “beginning” is used in various other texts similarly to describe the start of some period or career or course, such as the “beginning” of the Christian career of those to whom John wrote his first letter (1Jo 2:7; 3:11), the “beginning” of Satan’s rebellious course (1Jo 3:8), or the “beginning” of Judas’ deflection from righteousness. (Joh 6:64; see JUDAS No. 4 [Became Corrupt].) Jesus is the “only-begotten Son” (Joh 3:16) in that he is the only one of God’s sons, spirit or human, created solely by God, for all others were created through, or “by means of,” that firstborn Son.—Col 1:16, 17; see JESUS CHRIST (Prehuman Existence); ONLY-BEGOTTEN.

Spirit begettal, return to heavenly sonship. Jesus, of course, continued to be God’s Son when born as a human, even as he had been in his prehuman existence. His birth was not the result of conception by the seed, or sperm, of any human male descended from Adam, but was by action of God’s holy spirit. (Mt 1:20, 25; Lu 1:30-35; compare Mt 22:42-45.) Jesus recognized his sonship in relation to God, at the age of 12 years saying to his earthly parents, “Did you not know that I must be in the house of my Father?” They did not grasp the sense of this, perhaps thinking that by “Father” he was referring to God only in the sense that the term was used by Israelites in general, as considered earlier.—Lu 2:48-50.

However, about 30 years after his birth as a human, when he was immersed by John the Baptizer, God’s spirit came upon Jesus and God spoke, saying: “You are my Son, the beloved; I have approved you.” (Lu 3:21-23; Mt 3:16, 17) Evidently Jesus, the man, was then “born again” to be a spiritual Son with the hope of returning to life in heaven, and he was anointed by spirit to be God’s appointed king and high priest. (Joh 3:3-6; compare 17:4, 5; see JESUS CHRIST [His Baptism].) A similar expression was made by God at the transfiguration on the mount, in which vision Jesus was seen in Kingdom glory. (Compare Mt 16:28 and Mt 17:1-5.) With regard to Jesus’ resurrection from the dead, Paul applied part of Psalm 2 to that occasion, quoting God’s words, “You are my son, I have become your Father this day,” and he also applied words from God’s covenant with David, namely: “I myself shall become his father, and he himself will become my son.” (Ps 2:7; 2Sa 7:14; Ac 13:33; Heb 1:5; compare Heb 5:5.) By his resurrection from the dead to spirit life, Jesus was “declared God’s Son” (Ro 1:4), “declared righteous in spirit.”—1Ti 3:16.

Thus, it is seen that, even as David as a grown man could ‘become God’s son’ in a special sense, so, too, Christ Jesus also ‘became God’s Son’ in a special way, at the time of his baptism and at his resurrection, and also, evidently, at the time of his entrance into full Kingdom glory.

False charge of blasphemy. Because of Jesus’ references to God as his Father, certain opposing Jews leveled the charge of blasphemy against him, saying, “You, although being a man, make yourself a god.” (Joh 10:33) Most translations here say “God”; Torrey’s translation lowercases the word as “god,” while the interlinear reading of The Emphatic Diaglott says “a god.” Support for the rendering “a god” is found principally in Jesus’ own answer, in which he quoted from Psalm 82:1-7. As can be seen, this text did not refer to persons as being called “God,” but “gods” and “sons of the Most High.”

According to the context, those whom Jehovah called “gods” and “sons of the Most High” in this psalm were Israelite judges who had been practicing injustice, requiring that Jehovah himself now judge ‘in the middle of such gods.’ (Ps 82:1-6, 8) Since Jehovah applied these terms to those men, Jesus was certainly guilty of no blasphemy in saying, “I am God’s Son.” Whereas the works of those judicial “gods” belied their being “sons of the Most High,” Jesus’ works consistently proved him to be in union, in harmonious accord and relationship, with his Father.—Joh 10:34-38.