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Thursday, July 07, 2011

Junk DNA and Darwinism. Jonathan Wells and Plato suggest that you put them both into the dustbin.

The Procrustean presents a book review that summarizes the new Jonathan Wells book - The Myth of Junk DNA

"If Meyers taught us to read DNA, Wells teaches us to sing it."

Review : The Myth of Junk DNA

Myth of Junk DNA Jonathan Wells' The Myth of Junk DNA, is a well-written book that manages to accomplish two separate tasks: to silence the Darwinists who had claimed that recent genomic discoveries supported their dystopic version of The Signature in the Cell; and to bring all of us up-to-date on the breath-taking mysteries being decoded from this most ancient script.

He begins by picking up where Stephen Meyer left off, telling us that within each cell is this memory chip, this software program that directs everything we are and ever meant to be. When Watson and Crick decoded the DNA, there was great expectation that soon we would find the gene to every talent and attribute we had ever wished we had been born with. Sci-fi was filled with stories about a DNA pill that would turn you into a concert pianist, a ballerina, or a nuclear physicist, because the genes for all these talents could manually remedy what evolution had denied you. Soon a billion-dollar government program was begun to decode the human genome, after which, it was widely touted, we would find the cure to cancer and the common cold. The three billion base pairs of the human genome, it was thought, would hold genes stacked up cheek-to-jowl, together encoding some 100,000 different proteins. We knew how to count genes because we had already decoded the way the cell made protein, first by making RNA copies of the DNA, and then sending the RNA to the ribosome factory, which could identify the unique "start" and "stop" codes among the 64 different 3-letter "words" of the RNA software that marked the beginning and end of each gene.

After a decade of work and to everyone's great surprise, the human genome project found only 10,000 such start-stop pairs, suggesting that you and I are made out of fewer proteins than an amoeba! Furthermore, over 90% of the missing genes were DNA that apparently did nothing. Much of this "dark matter" was in long "stutter repeats" that couldn't even make a useful protein if you inserted the start and stop codons yourself. All that work, and nothing to show for it! Neither cancer nor the common cold was cured, and instead an even greater mystery was uncovered.

Wells carefully documents (with an extensive scientific bibliography) how a two-fold approach was taken to soften the blow. Scientifically, other genomes were transcribed and compared to ours, to see what were the essential parts common to all. Sophisticated techniques to "knock-out" chunks of DNA were also used (on animals) to see what happened when this non-protein-encoding DNA was taken out of commission. Simultaneously, the Darwinian "answer machine" was cranked up to explain why we should all have expected that 90% of our genome did nothing. (This, after earlier explaining how evolution made DNA the most efficient software ever discovered.) "Evolution is blind", we were told, and "junk DNA" is what you expect when random chance throws you together from odds and ends and doesn't know how to tell the difference between gold and dross. Furthermore, it looked as if some of the junk DNA was defunct viruses that had managed to multiply "infect" the DNA before being shut down by having their start-stop codons removed. And all this junk and scarred DNA, we were told, is evidence that no intelligence much less design had ever graced our genome.

Once again, Wells shows how the continued scientific efforts did not support "the myth of junk DNA." For if it really was useless, it should mutate rapidly and unrelated organisms should show almost no similarities in their junk. Instead, it was discovered that many sections of even stuttering repeats were conserved better than protein-encoding sections, suggesting it was doing something important. Furthermore, removing this DNA often caused death or deformity in the animals. More recently it was found that far from being junk, most of this 90% junk DNA was being transcribed into RNA, which is now found to be doing a myriad of jobs around the cell.

Wells goes on to list many of the jobs that "junk RNA" is doing, including turning on and off the ribosome, turning on or off the recycling of RNA, editing the RNA to produce up to 1000 different proteins from one "gene" of DNA, responding to external stimuli, defending the cell against attack, and generally providing an entire layer of control circuitry between DNA and proteins. More or less what you would expect from commissioned officers in a well-functioning army.

But this doesn't exhaust the utility of junk DNA. Wells goes on to suggest that DNA has mechanical properties needed when the cell divides and two identical copies of the DNA have to be separated into the respective daughter cells. The fibrils that pull the DNA have to attach somewhere, and one function of junk DNA is to provide a mechanical attachment. Further, two genes often have to be transcribed together, and their compact storage mechanism that has them all wound up like hose on a reel would prevent them from being close to each other. But by arranging the spacing by inserting junk DNA between them, the two genes can twist themselves to be immediately adjacent. However the most unbelievable use for junk DNA is found in the eyes of nocturnal mammals. Normally cells put their junk DNA (heterochromatin) out at the periphery of the nucleus, and the useful DNA (euchromatin) in the center, but in the retinal cells of these mammals, the denser junk DNA is clumped in the middle of the cell, so as to form a convex lens that pulls the light rays toward the center, and so focus even more light on the rods below. Junk DNA is acting as a night-vision goggle!

All these discoveries destroy the myth that evolution makes junk, and leaves us dumbfounded by the many overlapping and varied uses of this simple computer code. It would be as if you could make a telescope out of computer printouts, or fry an egg on your laptop. I'm sure the Darwin answer machine will eventually find a just-so story for this surprise, but in the meantime, Wells has me chortling at their speechless, gape-mouthed expression.

Yet even more spine-tingling is the sense that we are seeing truly dense information storage, something far more elegant than a Donald Knuth computer code. We expected to find something resembling our FORTRAN or machine-code assembly language, but instead we found something far more baroque, far more detailed, far more advanced than even Microsoft Windows. For in 3 Gigabytes, Microsoft barely gets Windows up and running for an expected lifetime of 5 years and it still must be patched monthly for the latest viruses, but in 3 Gigacodons, an entire baby is constructed with a full set of repairs for the assaults of countless viruses and the insults of an 80-year lifetime. If Meyers has shown the cell to have a software signature, then Wells has shown it to be written as poetry in an unknown tongue, replete with rhymes and stanzas and refrains and harmonies we can barely hear. If Meyers taught us to read DNA, Wells teaches us to sing it.

Highly recommended.


I am trying to patiently and slowly open the Darwinist mind to the concept that the cell is designed and that DNA is designed and that it is extreme foolishness to believe otherwise.  Engineers of all kinds are copying creation to improve motors, flight, fact what field of study has not benefited from copying a system from organisms?  Organisms had motors before we did, could fly, used echolocation, used complex algorithms to navigate and in fact to this day we are continuing to learn from God's design templates.  Despite the fact that this world is running downhill and organisms are collecting mutations and losing functions the cell is still astounding for its complexity and efficiency.  

Thanks to the (linked above) Procrustean blog.  Other worthwhile references:

Signature in the Cell: DNA and the Evidence for Intelligent Design


Fewer Mutations Means More Time


What does Plato have to do with design theory and debates over origins views? (ANS: A lot.)


Plato & Aristotle (Raphael)

The above challenge has been thrown down, in rather intemperate language accompanied by more outing misbehaviour.

It is revelatory on the depth of ignorance cultivated by the imposed dominance of evolutionary materialism via its cat’s paw, so-called methodological naturalism, in science education.

First, as was pointed out in the post on Plato’s warning on the amorality and ruthless factionism of evolutionary materialism day before yesterday,  Plato is one of the first to record the rise of evolutionary materialism as a worldview of origins and the nature of reality. In so doing, he plainly showed that the roots of such a view are philosophical rather than scientific, and in fact“evo mat” is thus shown to have the functionally equivalent status of a religion.

And yes, that means that the de facto establishment of evolutionary materialism in the public square and key institutions is tantamount to an undeclared establishment of the functional equivalent of a religion.
An issue that is already plainly of grave import.

We also need to understand that –  Lewontin, Coyne, the US NAS and NSTA among many others notwithstandingevolutionary materialism is not to be properly equated with “science,” it is but one of many possible worldviews for thoughtful people. And so, it must be able to stand on its own two legs in the teeth of comparative difficulties analysis. Including, on the challenge of grounding ethics by resolving the IS-OUGHT gap.

This is vital, as we all recognise that we have objective rights, which entail that we have duties to one another. As Arthur Holmes summarised:

If we admit that we all equally have the right to be treated as persons, then it follows that we have the duty to respect one another accordingly.  Rights bring correlative duties: my rights . . . imply that you ought to respect these rights. [Ethics: Approaching Moral Decisions (Downers Grove, IL: IVP, 1984), p. 81.]

So, immediately we can be confident that since evolutionary materialism has in its foundations no IS capable of supporting OUGHT, it cannot ground basic moral facts such as rights, and so is grossly factually inadequate.

That alone is sufficient to disqualify evolutionary materialism as a worldview for a great many thoughtful people.  It also sets the context in which we can see that some of these same people then can find good warrant for grounding their view of life in — at baseline level — a generic “Architect of the Cosmos” theism, that they may then build on in light of some tradition or another. (Cf. here.)

Including many scientists, starting with the likes of a Newton, or a Copernicus, or a Faraday or a Kelvin or a Pasteur and continuing down to today, including a significant number of Nobel Prize holders and other eminent scientists.

So, the atheistical assumption, boast and taunt — tracing to Dawkins –  that those who reject evolutionary materialism thereby prove themselves to be ignorant and/or stupid, and/or insane and/or wicked, is unwarranted, and even bigoted. Similarly, Dawkins’ outrageous assertion that those who raise their children in a theistic tradition are guilty of child abuse is outrageous.

Such should be dropped at once, and apologised for.

As for “outing” and “expelling behaviour” . . .  [Well, reread the Plato's warning post]
However, that is not our main focus this morning.

(BREAK IN TRANSMISSION: We did need to mop up the mess left by some outrageous behaviour culminating in mafioso style threats against my family. And BTW, a lie is a calculated or willful deception, not in effect anything that “I” disagree with. An example of a lie is the false and unwarranted accusation that I am a child abuser; which in my jurisdiction, would properly warrant a slander or libel charge.  Similarly, when one has been repeatedly corrected on it, to willfully insist that outing tactics culminating in we know you, we know where you are, and we know those you care for is not threatening behaviour, is tantamount to a lie. By contrast, to cite and expound on Plato’s expose of evolutionary materialism and resulting amorality and ruthless factionism, applying it to present circumstances is to teach corrective truth.)

Now, Plato identified key causal factors under the three key heads  necessity [phusis, "nature"], chance and art [techne], which we will for instance find directly reflected in Monod’s famous Chance and Necessity:

[[The avant-garde philosophers, teachers and artists c. 400 BC] . . . say that fire and water, and earth and air [[i.e the classical "material" elements of the cosmos], all exist by nature and chance, and none of them by art, and that as to the bodies which come next in order-earth, and sun, and moon, and stars-they have been created by means of these absolutely inanimate existences. The elements are severally moved by chance and some inherent force according to certain affinities among them-of hot with cold, or of dry with moist, or of soft with hard, and according to all the other accidental admixtures of opposites which have been formed by necessity. After this fashion and in this manner the whole heaven has been created, and all that is in the heaven, as well as animals and all plants, and all the seasons come from these elements, not by the action of mind, as they say, or of any God, or from art, but as I was saying, by nature and chance only . . .

As a bit of onward reading in The Laws, Bk X — or in this online discussion — would reveal, Plato, speaking in the voice of the Athenian Stranger (with a bit of help from Clenias), then went on to frame the central issue of design in worldview terms, actually making a cosmological design inference.  So, we may clip:

Ath. Nearly all of [the avant-garde], my friends, seem to be ignorant of the nature and power of the soul [[ = psuche, in effect the self-moved intelligent mind], especially in what relates to her origin: they do not know that she is among the first of things, and before all bodies, and is the chief author of their changes and transpositions. And if this is true, and if the soul is older than the body, must not the things which are of the soul’s kindred be of necessity prior to those which appertain to the body? 

Cle[nias]. Certainly.

Ath. Then thought and attention and mind and art and law will be prior to that which is hard and soft and heavy and light; and the great and primitive works and actions will be works of art; they will be the first, and after them will come nature and works of nature, which however is a wrong term for men to apply to them; these will follow, and will be under the government of art and mind. 

Cle. But why is the word “nature” wrong?

Ath. Because those who use the term mean to say that nature is the first creative power; but if the soul turn out to be the primeval element, and not fire or air, then in the truest sense and beyond other things the soul may be said to exist by nature; and this would be true if you proved that the soul is older than the body, but not otherwise.   [[ . . . .]

Ath. . . . when one thing changes another, and that another, of such will there be any primary changing element? How can a thing which is moved by another ever be the beginning of change? Impossible. But when the self-moved changes other, and that again other, and thus thousands upon tens of thousands of bodies are set in motion, must not the beginning of all this motion be the change of the self-moving principle? . . . . self-motion being the origin of all motions, and the first which arises among things at rest as well as among things in motion, is the eldest and mightiest principle of change, and that which is changed by another and yet moves other is second.

[[ . . . .]  Ath. If we were to see this power existing in any earthy, watery, or fiery substance, simple or compound-how should we describe it?

Cle. You mean to ask whether we should call such a self-moving power life?

Ath. I do.

Cle. Certainly we should.
Ath. And when we see soul in anything, must we not do the same-must we not admit that this is life?   [[ . . . . ]

Cle. You mean to say that the essence which is defined as the self-moved is the same with that which has the name soul?

Ath. Yes; and if this is true, do we still maintain that there is anything wanting in the proof that the soul is the first origin and moving power of all that is, or has become, or will be, and their contraries, when she has been clearly shown to be the source of change and motion in all things?

Cle. Certainly not; the soul as being the source of motion, has been most satisfactorily shown to be the oldest of all things. 

Ath. And is not that motion which is produced in another, by reason of another, but never has any self-moving power at all, being in truth the change of an inanimate body, to be reckoned second, or by any lower number which you may prefer?

Cle. Exactly.

Ath. Then we are right, and speak the most perfect and absolute truth, when we say that the soul is prior to the body, and that the body is second and comes afterwards, and is born to obey the soul, which is the ruler?   [[ . . . . ]

Ath. If, my friend, we say that the whole path and movement of heaven, and of all that is therein, is by nature akin to the movement and revolution and calculation of mind, and proceeds by kindred laws, then, as is plain, we must say that the best soul takes care of the world and guides it along the good path. [[Plato here explicitly sets up an inference to design (by a good soul) from the intelligible order of the cosmos.]

In short, Plato argues from the complex, beautiful, orderly functional organisation of the cosmos to its source in an intelligent agent, and that the careful organisation points to a good soul as that mind, guiding the cosmos along the good path. He roots this in a first discussion that rejects the notion of an infinite succession of blind material causes — and BTW (for those inclined to dismiss Plato), how does one traverse the infinite successively, step by step? — and points instead to a first cause, the self-moved, that when embodied we would term life, with a particular reference to intelligent, choosing, purposing life.

In doing so, he raises a very interesting turnabout: could it not instead be said that the real “nature” that goes on by itself is the good soul and architect of the cosmos, and that the rest, from the heavens to the earth and all that dwell in it, are the product of art?

Remember, we are not here discussing holy writ by a claimed prophet; we are looking at one of the first rank thinkers of all time, deeply reflecting on the implications of what he finds are key facts: blind succession of cause are not where we can find the first cause in the chain.

The self-moved, initiating cause that is usually termed “life” when we see it, especially intelligent, en-souled life.
The intelligible organisation of the cosmos calls for an explanation on such cause, in what we may term — Platonists, Thomists and others thinking about Plato’s Craftsman [Demiurge], forgive me, we are not able to go on to walking (much less running) yet, we must help those who have long needed to learn the rudiments of creeping first –  a “Cosmic Architect. ”

Now, we may disagree with Plato, and with those who think in related ways that may be distinct in important ways, e.g. Plato, at least nominally, was a pagan [nb, his subtle disclaimers at the head of this discussion make that "nominally" a potentially key word]. But, we must learn some basic respect: such a manner of thinking is not to be dismissed, or derided and caricatured in ugly ways. 

To further underscore my point, here is Newton in his — again, suspiciously neglected — General Scholium to Principia:

. . . This most beautiful system of the sun, planets, and comets, could only proceed from the counsel and dominion of an intelligent and powerful Being. And if the fixed stars are the centres of other like systems, these, being formed by the like wise counsel, must be all subject to the dominion of One; especially since the light of the fixed stars is of the same nature with the light of the sun, and from every system light passes into all the other systems: and lest the systems of the fixed stars should, by their gravity, fall on each other mutually, he hath placed those systems at immense distances one from another.

This Being governs all things, not as the soul of the world, but as Lord over all; and on account of his dominion he is wont to be called Lord God pantokrator , or Universal Ruler . . . And from his true dominion it follows that the true God is a living, intelligent, and powerful Being; and, from his other perfections, that he is supreme, or most perfect. He is eternal and infinite, omnipotent and omniscient; that is, his duration reaches from eternity to eternity; his presence from infinity to infinity; he governs all things, and knows all things that are or can be done . . . [.]

Every man, so far as he is a thing that has perception, is one and the same man during his whole life, in all and each of his organs of sense. God is the same God, always and every where. He is omnipresent not virtually only, but also substantially; for virtue cannot subsist without substance. In him are all things contained and moved [i.e. cites Ac 17, where Paul evidently cites Cleanthes]; yet neither affects the other: God suffers nothing from the motion of bodies; bodies find no resistance from the omnipresence of God. It is allowed by all that the Supreme God exists necessarily; and by the same necessity he exists always, and every where. [i.e accepts the cosmological argument to God.] Whence also he is all similar, all eye, all ear, all brain, all arm, all power to perceive, to understand, and to act; but in a manner not at all human, in a manner not at all corporeal, in a manner utterly unknown to us. As a blind man has no idea of colours, so have we no idea of the manner by which the all-wise God perceives and understands all things. He is utterly void of all body and bodily figure, and can therefore neither be seen, nor heard, or touched; nor ought he to be worshipped under the representation of any corporeal thing. [Cites Exod 20.] We have ideas of his attributes, but what the real substance of any thing is we know not. In bodies, we see only their figures and colours, we hear only the sounds, we touch only their outward surfaces, we smell only the smells, and taste the savours; but their inward substances are not to be known either by our senses, or by any reflex act of our minds: much less, then, have we any idea of the substance of God. We know him only by his most wise and excellent contrivances of things, and final cause [i.e from his designs]: we admire him for his perfections; but we reverence and adore him on account of his dominion: for we adore him as his servants; and a god without dominion, providence, and final causes, is nothing else but Fate and Nature. Blind metaphysical necessity, which is certainly the same always and every where, could produce no variety of things. [i.e necessity does not produce contingency] All that diversity of natural things which we find suited to different times and places could arise from nothing but the ideas and will of a Being necessarily existing. [That is, implicitly rejects chance, Plato's third alternative and explicitly infers to the Designer of the Cosmos.] . . . [.]

And thus much concerning God; to discourse of whom from the appearances of things, does certainly belong to Natural Philosophy.

In short, Newton’s thought is clearly hebraic and related to Plato’s ideas, and he infers from the intelligible, functional, complex organisation of the observed cosmos to its source in an intelligent, necessary being whose word is the law of the cosmos that men discover. Indeed, he actually holds that to discourse upon that Architect in light of the appearances of things is a legitimate act within natural philosophy; the older name for especially the physical sciences.  That is, it is the worldview right of the scientist to look up from his observations and calculations, and to reflect soberly on what lies behind the wonderful order and beauty he sees.

With that history of ideas in mind, and with the sobering considerations already on the table, it is plainly time for a serious re-think on how these sorts of themes are being treated in our civilisation today. And, particularly, we should reflect on the role being played by ruthless factions that have set out to shout down and intimidate  any and all who would dare think out side of their preferred evolutionary materialist box.

Then, we should have the courage to think for ourselves, and to take a bold stance, exposing those who would impose worldviews censorship on science, science education and science-related public policy.