@pauluc: Your essential argument is a strawman argument. You critize …

Comment on The End of “Junk DNA”? by Sean Pitman.


Your essential argument is a strawman argument. You critize a caricature of the science of genetics and molecular biology and do not seem to be engaged with the basic ideas. For sure there have been profound errors and lack of understanding but that is what science is like. Increasing understanding is expected as new methods and data become available. Hypothesis testing is about detecting error and you are absolutely correct in that the “junk” DNA hypothesis as presented in the popular press has been rejected.

It wasn’t just a “popular press” idea. The “junk DNA” concept was part of mainstream science for decades . . . a prediction of neo-Darwinism according to many biologists.

But it was not at all rejected because some armchair scientists denied it on a priori grounds but was rejected because of new data, experiments and better models.

The point is that there was more than enough data decades ago to reject the junk DNA concept. The only reason the junk DNA concept held on as long as it did is because of neo-Darwinian predictions for it. One clue that should have raised questions long ago is that it is very expensive for a living thing to maintain DNA. It just doesn’t, and didn’t, make any sense for natural selection to avoid getting rid of something that really didn’t contribute substantially to the immediate survival of the organism. The arguments that junk DNA was maintained by nature in order to provide potential future evolutionary benefits to the population didn’t make much sense because nature has no such foresight. Nature only selects, in a positive manner, for what works right now in some kind of beneficial way.

There has been increase in understanding of genomics and the role of junk DNA but as Tim Standish breathlessly says evolutionary concepts were used both for the earlier understanding of “non-protein-coding” DNA as padding and a repository of potential reusable but unnecessary genetic information and for the newer concept of selection of functional activity found in these regions not coding for protein.

Yes yes. But “junk DNA” was thought to have no significant active role in phenotypic expression or the control of genes in a manner that could be positively selected by nature. The view that non-coding DNA was simply a junk-yard “repository” that could be used for future evolutionary advantages is now known to be painfully mistaken – and should have been detected as such long ago.

On the other hand, the design model or paradigm for living things and their informational complexity was predictive in this case while the naturalistic perspective actually slowed down scientific advancement in this area.

3] You seem to believe that molecular geneticists before you and fellow young earth creationists came along with vague statements in the blogoshere about function of the whole of the genome, believed that junk DNA (as Gould rightly observes a “disrespectfully” denoted shorthand predicated on the prokaryotic model of funtional genes) was completely useless.

I think my statements and the statements of many other IDists were quite clear regarding the active functionality of most non-coding forms of DNA and the eventual discovery of such. Also, I never said that naturalists thought “junk DNA” to be absolutely functionless. Obviously, as I originally noted, Gould believed that “junk DNA” had a repository “function”, but he did not believe that it had an active function in living things. He did not believe that it had any significant control over the expression of genes and the overall phenotype of the organism. He was very much mistaken.

This is patently wrong. If you read even the abstract of the 1988 paper from John Bodnar “A domain model for eukaryotic DNA organization: A molecular basis for cell differentiation and chromosome evolution” J theoretical biol 1988, that is cited in the paper by William Dembski that you then cite, you will see that Bodnar was advocating consideration of the genomic organization in terms of “domains” that are much more complex than simply the promoters and coding exons assumed to be subject to evolutionary selection. This essential idea that the genome has been selected by the resultant phenotype has changed little in the last 50 years. The idea that a phenotype is the basis of selection not the genotype has gained increasing recognition as the complexity of the genome and the many levels of regulation and control has become evident. Increasing understanding of “Junk DNA” and the highly nuanced regulation of structure and function determined by regions outside conventional coding regions has enhanced neo-darwinian models premised on natural selection rather than destroyed them as you seem to hope based on your models of reality.

Hardly. Selection has to be based on the phenotypic level. Nature cannot “see” anything at the genotypic level that is not expressed at the phenotypic level. Creationists have long recognized this concept – in the face the claims of naturalists like Richard Dawkins who have promoted selection on the genotypic level.

The regulatory function and structure of non-coding DNA does not help explain the evolution of novel functional systems and elements within any gene pool beyond very very low levels of functional complexity. What the discovery of the functionality of non-coding DNA has done is show that the neo-Darwinian predictions were wrong regarding its value and they were wrong regarding the detrimental mutation rate. This second error will prove far more devastating to neo-Darwinism than the first.

4] You do not seem to make any distinction between the protein coding and non-protein coding regions in terms of their contribution to phenotype.

I thought I was very clear in my article that there is quite a significant difference here. Protein-coding genes are the basic building blocks, the basic “bricks and mortar” so to speak. How these bricks and mortar are used to build different kinds of structures or living things is dependent upon the information in the non-coding regions of the genome where the real blueprint resides.

You seem to be suggesting all are essential. Do you really believe that?

You don’t think non-coding DNA essential to complex living things that depend upon many multicellular organ systems? Are you serious? We aren’t talking about single-celled bacteria here. While not all forms of non-coding DNA are created equal, non-coding DNA contains the primary information for phenotypic expression, dictating how the coding genes are to function and what type of organism to build.

Are all pseudogenes functional?

No. There are true pseudogenes that have in fact lost their original functionality.


What do you mean by “critical”? Critical to life? Consider that you can lose a lot of body parts that aren’t critical to life that you wouldn’t want to just throw away as “non-critical”. I dare say that you’d still like to keep your arms and legs and colon and bladder, etc . . . even though you could live on without them for quite some time.

Surely processed pseudogenes are evidence that introns are non-essential.

Again, non-essential to what? Many intronic regions are now known to carry out important functions (Link 1, Link 2, Link 3). Just because you may be able to survive without some of them doesn’t mean much when it comes to determining important functionality. Ironically, yours is the same argument that was used by many evolutionists to suggest that non-coding DNA was functionless “junk” – because much of it could be deleted without apparent detriment to the organism. Well, that notion turned out to be wrong. The truth is that “Introns in contemporary species fulfill a broad spectrum of functions, and are involved in virtually every step of mRNA processing.” (Link).

Consider also the following comments regarding intron functionality:

As a first approximation, it is possible to view introns as unimportant sequences whose only function is to be removed from an unspliced precursor RNA in order to generate the functional mRNA, rRNA or tRNA product. However, it is now well-established that some introns themselves encode specific proteins or can be further processed after splicing to generate noncoding RNA molecules. Alternative splicing is widely used to generate multiple proteins from a single gene…

Alternative splicing of introns within a gene acts to introduce greater variability of protein sequences translated from a single gene, allowing multiple related proteins to be generated from a single gene and a single precursor mRNA transcript. The control of alternative RNA splicing is performed by complex network of signaling molecules that respond to a wide range of intracellular and extracellular signals.

Introns contain several short sequences that are important for efficient splicing, such as acceptor and donor sites at either end of the intron as well as a branch point site, which are required for proper splicing by the spliceosome. Some introns are known to enhance the expression of the gene that they are contained in by a process known as intron-mediated enhancement (IME).


So you see, just because you can live without something doesn’t mean it isn’t useful or beneficial or otherwise relevant to better phenotypic functionality.

Are alu repeats critical and essential?

Alu repeats are also known to be functionally important. “Dynamic and functional Alu repeats seem to be centrally placed to modulate the transcriptional landscape of human genome” (From ‘JUNK’ to Just Unexplored Noncoding Knowledge: the case of transcribed Alus, 2012).

Is the genome uniformly critical and functional? Is there a heirarchy with protien coding at the top and supporting scaffolding and microregulatory and integrative regions below.

There certainly is a hierarchy with different areas having more or less “critical” functionality. However, I would put protein-coding genes at the bottom, not the top, in this hierarchy of functionality. In this, even the likes of John Mattick seem to agree with me:

“Indeed, what was damned as junk because it was not understood may, in fact, turn out to be the very basis of human complexity,” Mattick suggests. Pseudogenes, riboswitches and all the rest aside, there is a good reason to suspect that is true. Active RNA, it is now coming out, helps to control the large-scale structure of the chromosomes and some crucial chemical modifications to them—an entirely different, epigenetic layer of information in the genome.”

Wyatt Gibbs, The Unseen Genome: Gems among the Junk, Scientific American, November 2003, pp 45-53

Did you read what I read? Mattick himself argues that non-coding DNA forms the very basis of human complexity? way back in 2003? It’s only gotten more convincing since then…

What precisely is your model based on intelligent design? I cannot seem to find it articulated in a scientific way.

Upon what basis must intelligent design be invoked to explain anything in a “scientific way”? – any artifact? What are SETI scientists looking for and how will they know when they’ve discovered evidence of ET? The very same arguments can be used to invoke ID behind certain features of living things. If a given phenomenon goes well beyond what any known mindless force of nature can explain in a reasonable amount of time, and if that phenomenon is within the creative powers of intelligent agents (i.e., humans), then the most rational conclusion is that the origin of this particular phenomenon was most likely intelligent on at least the human level of intelligence or beyond.

What about junk RNA? Will this ongoing post ENCODE scientific debate be the source for your next blog? Would you like to articulate your view based on a YEC perspective with such specificity that we can see if you are right or wrong?

My position is testable in a potentially falsifiable manner. All you have to do is produce a mindless naturalistic mechanism that can create qualitatively novel systems at higher levels of functional complexity in a reasonable amount of time – or at least a tenable statistic model for such. So far, the very best you have is just-so stories and a lot of bravado. Where’s the science?

It is easy to sit at your study desk and pontificate post hoc on the errors of evolutionary biologists but to be credible as a scientist you need to propose hypotheses with some specificities and test them against the data.

You need to get off your high horse and actually test your naturalistic just-so stories against reality – in a statistically relevant manner (i.e., using some real mathematical models that are statistically relevant and meaningful). This you have yet to do.

You yourself admit that you aren’t about to test your notions regarding the Darwinian mechanism of random mutations and natural selections in any statistically relevant way. You say that you “approach the reality of speciation in a top down fashion the same way as Darwin did” (Link). Because of this you do not recognize any specific limitation to “speciation” or change over time. You don’t actually consider or recognize the statistical potential and/or limitations of Darwin’s mechanism of random mutations and natural selection when it comes to creativity at various levels of functional complexity. That is why you’re not doing real science here. Your position is immune to even the potential of falsification since it cannot be tested – not even statistically. All you have are just-so stories beyond very low levels of functional complexity.

My position, on the other hand, is open to such testing and potential falsification.

Sean Pitman

Sean Pitman Also Commented

The End of “Junk DNA”?

It does seem like this feature would probably have an effect on the odds, but I’m not sure what additional significance this would bring to the table since the odds of evolving anything qualitatively novel that requires a minimum of more than 1000 specifically arranged amino acid residues would require trillions upon trillions of years of time.

Sean Pitman

The End of “Junk DNA”?

What is clearly not acceptable is that there is generation of any new “information” as that would clearly play into the hands of the evolutionists. As we discussed in detail concerning the vast predominance of allelic variation in canids and man that must have arisen de novo from the breeding pair or breeding 5 do you or do you not think that new allelic variation contains new “information”?

The vast majority of allelic mutational changes do and did not produce qualitatively new information – only changes to the degree of expression of pre-existing systems (i.e., more or less of the same thing). More or less of the same thing isn’t what I would call “new” information.

However, there are relatively rare examples of truly new information that is qualitatively unique entering the gene pool. The problem, of course, is that all such examples are at very very low levels of functional complexity (i.e., requiring less than 1000 specifically arranged amino acid residues).

So, its relatively easy to evolve a novel beneficial system that is based on a specified 3-character sequence. It’s exponentially harder to evolve a truly novel system that is based on a minimum of 20 specified characters. And, it is effectively impossible to evolve a qualitatively novel system that requires at least 1000 specifically arranged characters (regardless of the type of information system you’re dealing with).

If you say yes then you are certainly outside the current YEC convention. If you say no then you are suggesting that species with very different phenotypes can evolve without any new information. A position that most biologist would find surprising.

I have been invited to speak in numerous venues, to include those largely populated by YECs and YLCs – as you can imagine. Yet, after I present evidence for low-level evolution the vast majority of creationists I’ve spoken to respond very favorably – even enthusiastically. After all, it simply makes good sense that the random discovery of novel beneficial sequences within sequence spaces would be exponentially easier to achieve when you’re dealing with 3-character sequences vs. 20 character sequences. It just makes sense to most people – including well-educated creationists.

Sean Pitman

The End of “Junk DNA”?

You tout reason as trumping faith but do not appear to see that the enlightenment enterprise took precisely the position you think desirable.

I didn’t say that reason trumps faith. What I said was that faith does not trump reason. There’s a difference. What I’ve also said many times in this forum is that a useful or rational faith must go hand in hand with reason. One cannot exist in any kind of meaningful or useful way without the other. Even science itself is dependent upon making leaps of faith into that which is not absolutely known or knowable. Faith and reason are equals in my mind, both created by God. I believe that God gave us our reasoning minds for a reason and He does not expect us to then forgo its use (to paraphrase Galileo).

The logical and consistent end of that road is nihlism. That people like Richard Dawkins and the new atheists unlike the old atheists arrived at a faith position of meaningfulness in humanism rather than meaningless nihlism I think reflects the essential desire in all man for meaning and some higher meaning or faith.

There is no doubt that all mankind desires meaning. However, a desire for meaning is just wishful thinking if desire isn’t backed up by evidence. The same is true for faith. Faith, without the backing of evidence-based reasoning is nothing but wishful thinking.

Also, if God is the God of reason as well as faith, the honest and sincere use of the Divine gift of reason will lead one toward the God of reason; not nihilism.

“You will seek me and find me when you seek me with all your heart.” – Jeremiah 29:13 NIV

Motivation is vital, but given the sincere motivation of the heart, the Divine miracle is that God steps in and interacts with Human reasoning capabilities to guide the mind, based on evidences He has provided, toward Himself. God never asks for acts of faith without first providing evidence as a rational basis for the act or leap of faith. We are even asked to test various claims, to “test the spirits” to see what is and what isn’t from God. (1 John 4:1 NIV) Throughout the Bible God is constantly providing evidence as a basis for His claims and a reason to follow, serve, and worship Him. Nowhere is God portrayed as expecting blind faith in any naked claim coming from His mouth. The claims are always backed up by some form of evidence or prior experience with God and evidence of who He claims to be.

God understands the importance of evidence and the natural human desire for evidence. After all, He’s the one who made us this way.

Sean Pitman

“I do not feel obliged to believe that the same God who has endowed us with senses, reason, and intellect has intended us to forgo their use and by some other means to give us knowledge which we can attain by them.” – Galileo Galilei

Recent Comments by Sean Pitman

Science and Methodological Naturalism
Very interesting passage. After all, if scientists are honest with themselves, scientific methodologies are well-able to detect the existence of intelligent design behind various artifacts found in nature. It’s just the personal philosophy of scientists that makes them put living things and the origin of the fine-tuned universe “out of bounds” when it comes to the detection of intelligent design. This conclusion simply isn’t dictated by science itself, but by a philosophical position, a type of religion actually, that strives to block the Divine Foot from getting into the door…

Revisiting God, Sky & Land by Fritz Guy and Brian Bull

Why is it that creationists are afraid to acknowledge the validity of Darwinism in these settings? I don’t see that these threaten a belief in God in any way whatsoever.

The threat is when you see no limitations to natural mindless mechanisms – where you attribute everything to the creative power of nature instead of to the God of nature.

God has created natural laws that can do some pretty amazing things. However, these natural laws are not infinite in creative potential. Their abilities are finite while only God is truly infinite.

The detection of these limitations allows us to recognize the need for the input of higher-level intelligence and creative power that goes well beyond what nature alone can achieve. It is here that the Signature of God is detectable.

For those who only hold a naturalistic view of the universe, everything is attributed to the mindless laws of nature… so that the Signature of God is obscured. Nothing is left that tells them, “Only God or some God-like intelligent mind could have done this.”

That’s the problem when you do not recognize any specific limitations to the tools that God has created – when you do not recognize the limits of nature and what natural laws can achieve all by themselves.

Sean Pitman

Revisiting God, Sky & Land by Fritz Guy and Brian Bull
@Bill Sorensen:

Since the fall of Adam, Sean, all babies are born in sin and they are sinners. God created them. Even if it was by way of cooperation of natural law as human beings also participated in the creation process.

God did not create the broken condition of any human baby – neither the physical or moral brokenness of any human being. God is responsible for every good thing, to include the spark or breath of life within each one of us. However, He did not and does not create those things within us that are broken or bad.

“The owner’s servants came to him and said, ‘Sir, didn’t you sow good seed in your field? Where then did the weeds come from?’ ‘An enemy did this,’ he replied. “The servants asked him, ‘Do you want us to go and pull them up?'” Matthew 13:27-28

Of course, all humans are indeed born broken and are in a natural state of rebellion against God. However, God is not the one who created this condition nor is God responsible for any baby being born with any kind of defect in character, personality, moral tendency, or physical or genetic abnormality. God did not create anyone with such brokenness. Such were the natural result of rebellion against God and heading the temptations of the “enemy”… the natural result of a separation from God with the inevitable decay in physical, mental, and moral strength.

Of course, the ones who are born broken are not responsible for their broken condition either. However, all of us are morally responsible for choosing to reject the gift of Divine Grace once it is appreciated… and for choosing to go against what we all have been given to know, internally, of moral truth. In other words, we are responsible for rebelling against the Royal Law written on the hearts of all mankind.

This is because God has maintained in us the power to be truly free moral agents in that we maintain the Power to choose, as a gift of God (Genesis 3:15). We can choose to accept or reject the call of the Royal Law, as the Holy Spirit speaks to all of our hearts…

Remember the statement by Mrs. White that God is in no wise responsible for sin in anyone at any time. God is working to fix our broken condition. He did not and does not create our broken condition. Just as He does not cause Babies to be born with painful and lethal genetic defects, such as those that result in childhood leukemia, He does not cause Babies to be born with defects of moral character either. God is only directly responsible for the good, never the evil, of this life.

Sean Pitman

Revisiting God, Sky & Land by Fritz Guy and Brian Bull

Again, your all-or-nothing approach to the claims of scientists isn’t very scientific. Even the best and most famous of scientists has had numerous hair-brained ideas that were completely off base. This fact does not undermine the good discoveries and inventions that were produced.

Scientific credibility isn’t based on the person making the argument, but upon the merits of the argument itself – the ability of the hypothesis to gain predictive value when tested. That’s it.

Sean Pitman

Gary Gilbert, Spectrum, and Pseudogenes
Don’t be so obtuse here. We’re not talking about publishing just anything in mainstream journals. I’ve published several articles myself. We’re talking about publishing the conclusion that intelligent design was clearly involved with the origin of various artifactual features of living things on this planet. Try getting a paper that mentions such a conclusion published…

Sean Pitman