@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”?

Lots of non-Adventist individuals and organizations are committed to Jesus Christ – like the Catholics, Baptists, Lutherans, Mormons, etc. However, the simple criteria of being committed to one’s own personal view of Jesus Christ does not qualify one as being a paid representative of the Seventh-day Adventist Church.

Now, this isn’t to say that being committed to Jesus Christ and His example, as detailed in the Bible, isn’t a good thing. It’s a very very good thing and the motive of love behind such a decision is the very basis of salvation. However, even being in a saving relationship with Jesus is not enough to qualify an individual to be an effective representative of the Seventh-day Adventist Church in particular.

The Adventist Church takes on basic Christianity as well as an additional mission – a mission which includes upholding before the world some 28 doctrinal beliefs which the church considers “fundamental” or crucial to its primary goals and mission during the last days of Earth’s history.

Now, one may be saved without being a part of the Adventist mission or church – thank God! In fact, the vast majority of people who will be saved in Heaven one day will never have even heard of Seventh-day Adventists. So, this isn’t an issue of salvation. It is an issue of appropriately representing the primary goals and mission of an organization as that organization defines itself.

You, weather you like it or not, are not in line with many of the primary goals and ideals of the Seventh-day Adventist Church. That doesn’t make you good or bad or outside of the saving love and grace of God. It just means that you cannot adequately represent the Seventh-day Adventist Church as a paid representative. Your representation would be counterproductive to the stated goals and missions of the church as an organization.

That is why it would be much better for you, and for more honest, if you were to take on a label that more accurately represents your current world views…

Sean Pitman

The End of “Junk DNA”?
@Professor Kent:

When empirical evidence and God’s word go different directions, you will choose the evidence, whereas the SDA Church always has and always will prioritize God’s word.

During the founding of the Seventh-day Adventist Church the founding fathers took on the position that the Bible prophesied that Jesus would return in 1844. The empirical evidence proved this notion wrong. And, these founding fathers were forced, by the empirical evidence, to admit that their faith in what they thought the Bible said was mistaken.

You see, the SDA Church, from its very beginnings, has been forced to recognize the interplay between faith and evidence for the rational mind. One cannot rationally argue that one’s faith in what one thinks the Bible says, or even the origin of the Bible, is entirely independent of the weight of empirical evidence.

It is for this reason that the modern Seventh-day Adventist Church is actually concerned over what is being taught at La Sierra University regarding the topic of origins. If all that mattered was a fideistic faith in the Bible and our own special interpretation of the Bible, the church wouldn’t care what people thought of the empirical evidence. It wouldn’t care what was being taught in science classes within its own schools. This simply isn’t the case.

You are delusional to believe that the SDA Church will agree to disembody and disavow itself of God if the accumulated evidence goes against its present interpretation of scripture.

But the church has changed its mind before regarding its views of the Bible based on the weight of empirical evidence (as noted above).

Again, God does not ask us to believe or have faith without the weight of evidence. He does not expect us to believe in something that has no more evidential backing than the Tooth Fairy or Santa Claus. That simply wouldn’t be reasonable on the part of God nor would it be fair for Him to act in such a manner…

Sean Pitman

The End of “Junk DNA”?

There is a great gulf between You and I. Where does one start in trying to find common ground and responding to your very concrete thought structure. Its as if the last 200 years have not happened. Your view of natural theology may have been accepted by William Paley but is not an approach to God thought valid by most modern theologians with any acquaintance with science.

One of the problems I personally have with your perspective, and that of many modern theologians, is that it seems to me to be inconsistent with itself. You yourself describe your own position as “irrational”! You reject the authority of the Scriptures when the Biblical authors describe the miracle of God creating life on this planet in just six literal days (clearly what the author of the Genesis account was trying to convey to his readers)… because of what you view as the contrary evidence of modern science. Yet, at the very same time, you accept the claims of the Biblical authors when they describe the miraculous virgin birth, life, death, and Resurrection of Jesus. You accept this portion of the Scriptures contrary to the claims of the vast majority of modern scientists who claim that such things are impossible.

Does this not then mean that your internally derived “faith” allows you to pick and choose what you will and will not believe independent of the influence of anything else? It isn’t a matter of consistent Biblical interpretation for you because you simply aren’t consistent in how you interpret the Bible or determine what is or isn’t true. You pick and choose based on your own individual desires for what you want to be true. That is why your faith is inconsistent with itself and is, as you yourself explain, completely irrational to the point of overt fideism. You take on a form of fideism that is its own evidence independent of any influence outside of your own mind and your own feelings and desires – to include any consistent influence from the Bible itself.

What argument can you or any modern theologian present to make what you yourself claim is an irrational position appear remotely attractive to those who appreciate rational thought and careful consistent investigation of fantastic claims?

It is not the 19th century and we are called to preach the grace of God to a secular world. Your vision shows no imagination or understanding of spirituality or the reality and value of vision, myth and abstract concepts that may have no correspondence in concrete realities.

But I do find value in various myths, legends, allegories, and fairytales. Even Jesus used such stories to teach various truths about the existence of realities that are not yet seen. However, it makes a great deal of difference if one believes that the life, death, and resurrection of Jesus is a good moral fable vs. true empirical historical reality. If the disciples of Jesus had believed His claims to be the Son of God simply allegorical, rather than empirical reality, they would not have put their own lives on the line. No rational person, who is naturally prone to avoid a martyr’s death, is going to put his life on the line for stories that he believes are mythical or allegorical – devoid of any “correspondence with concrete realities”.

They key point here is that if Jesus had not been raised from the dead and His disciples had not personally witnessed the empirical reality of this event, there would be no Christian Church of any kind today. All of Christian faith hinges on the literal reality of the Resurrection. Without this reality, there is no mystical experience with God that can rationally support the claims of Christianity.

Do you agree with Martin Luther in his statement about scripture trumping observation:

“People gave ear to an upstart astrologer who strove to show that the earth revolves, not the heavens or the firmament, the sun and the moon. Whoever wishes to appear clever must devise some new system, which of all systems is of course the very best. This fool [or ‘man’] wishes to reverse the entire science of astronomy; but sacred Scripture tells us that Joshua commanded the sun to stand still, and not the earth.”
– Martin Luther, Table Talk

If you truly privilege scripture over science you should really revamp this web site to be consistent with the supremacy of scripture along the lines of the site http://www.fixedearth.com/ A site that is at least absolutely consistent with biblical literalism as Luther saw it.

Even though we who live in this modern age know that the Earth does in fact revolve around the Sun, we still speak in everyday terms as the Sun “rising in the east” and “setting in the west” or the “Sun going down”. Such are terms of perspective. In context, therefore, no further interpretation is necessitated in the Bible’s description of Joshua speaking from his own Earth-bound perspective. Surely you can understand the difference between such passages and passages in Genesis where it would be very very difficult to misinterpret the observation of “evenings and mornings” separating the “days” of creation – regardless of perspective. In such passages the author is clearly claiming that God showed him that the days of creation were separated by what clearly appeared to be “evenings and mornings” from his Earth-bound perspective. There’s a big difference here.

As far as Martin Luther is concerned, he was a great reformer and he did advance important truths for his time. However, he was no prophet and received no privileged revelation regarding such things. He forwarded and acted upon a great many points of misunderstanding regarding the meaning of many Scriptural truths which the Seventh-day Adventist Church has since realized – to include those truths revealed to us by God speaking in a very privileged manner through Ellen White.

Now, you can either accept or reject the Adventist perspective on such things, but it is very difficult to call yourself an Adventist or a true representative of the Seventh-day Adventist Church when you are actually fighting against numerous doctrinal ideals that the Adventist Church, as an organization, still holds to be fundamentally important. It would be much better and far more honest for you to describe yourself in terms that more accurately reflect your true beliefs.

The reality however is that both you and I interpret the scriptures. As I have said before you appear to practice naturalistic evidence based medicine contrary to the biblical description of healing but then pretend that you are following the plain text of scripture when reject entirely naturalism when it comes to origins. You claim;

“You pick and choose what elements you will use to build your own image of “christianity”… which is quite different from the Biblical claims.”

But do not at all seem able to see that you are in fact doing exactly what you project in accepting evidence based medicine contrary to a plain reading of scripture but claiming origin by divine fiat and miracle on the basis of one particular reading of scripture.

There is actually good support for evidence-based medicine in Scripture. Just because the Scriptures also point out the power of prayer and God’s willingness to supernaturally intervene, on occasion, in our lives does not mean that the Scriptures are opposed to evidence-based medicine. Such a notion is completely contrary to the position of the Bible, Mrs. White, and the Adventist Church on the topics of health and medicine in general where the laws of nature, set in place by God, are to be dealt with on a routine basis in the practice of medicine and healthful living.

You continue to misconstrue the point of my discussion of Santa Claus and Christmas. Children can and do grow in their understanding of reality and are able to see beyond the concrete events of Christmas to see it as a representation of a worthy abstraction that is not invalidated by rejecting a fictitious Santa Claus. You seem unable to move from the concrete to the abstract and yet again claim you will reject Christ if your biblical interpretation is found not to be consistent with a simplistic reality. As though your superior mind trumps any non-rational revelation of God.

A non-rational revelation of God would not, by definition, make rational sense – right? (any more than a desire to believe in the reality of existence of Santa Claus or the Flying Spaghetti Monster?) Why then should I believe in any irrational “revelation” that makes no sense to me? Can you provide any rational answer to this question? Wouldn’t any response you might submit be irrational by definition? That’s why your position makes no sense to me. Why even try to argue for what you yourself are arguing has no rational explanation?

Your arrogance is unceasingly amazing.
You claim:

“And, so far, the organized Adventist Church agrees with me. Of course, you can call yourself whatever you want. But, again, that doesn’t mean that the church is going to recognize your claims as actually representing the church’s view of reality. So, why would you expect anyone holding views that undermine the fundamental goals and ideals of the church, the ‘fundamental beliefs’, to be paid by the church”

You are of course right if you think the church that is being rebuilt by Ted Wilson and Clifford Goldstein with their militant fundamentalism and unsavoury and ungracious political manouvering is the legitimate heir of traditional Adventism but I do not.

Where did Ted Wilson or Clifford Goldstein set up the fundamental doctrinal ideals of the Seventh-day Adventist Church? You give them far too much credit! These fundamentals were set up well before they came on the scene…

At the very least, you must admit that you are strongly opposed to many of the clearly stated doctrinal positions that the Seventh-day Adventist Church has long held, and currently holds, to be “fundamental” to its very existence. You fundamentally disagree with both the founders and the current leaders of the church on many key points of doctrine. You disagree with many of the modern and historical doctrinal positions of the SDA Church as an organization.

You are really more of a “social Adventist” who was raised in the Adventist Church but who really doesn’t subscribe to many of the doctrinal positions of the church as an organization. Why then do you wish to continue to take on the title of “Seventh-day Adventist” when this title doesn’t really do you justice? – when it doesn’t truly represent who you really are and what you really believe? And, why on Earth would you expect anyone who holds similar views to your own to be hired by any organization who claims to be fundamentally opposed to what you actually believe and are willing to teach/preach?

Wouldn’t it be far more honest and ethical for you and those of like mind to more clearly present yourselves and what you stand for and then go and work for those who are more than willing to pay to have such ideas taught in their schools and preached from their pulpits? Why the aversion to completely open and honest transparency here?

And, if the Seventh-day Adventist Church, as an organization, really has no problem with those from your perspective preaching and teaching on the church’s dime, why then hasn’t the Adventist Church come out in open support of such efforts? Why has the Adventist Church, as an organization, gotten so worked up over Neo-Darwinism being so openly promoted as La Sierra University? – if the church really is as supportive of your position as you seem to suggest?

Sean Pitman

Recent Comments by Sean Pitman

The Creator of Time
It’s been enjoyable having you. I wish you all the best. Someday, if I’m right, everything will be made clear and you will see your Maker face-to-face. Of course, if I’m wrong, neither one of us will be the wiser…

By the way, I am not a “young Earth creationist” or “YEC”, but something a bit different – a young life creationist (YLC). Of course, from your perspective it makes little difference. 😉

The Creator of Time
A “Rational Wiki” quote? – about proof and disproof? 😉

First off, science isn’t about absolute proof, but the weight of evidence. Nothing can be absolutely proved in science – only disproved. The power of science is in the ability for the hypothesis in question to resist disproof, thereby gaining predictive value. This means, of course, that a valid scientific hypothesis must be testable in a potentially falsifiable manner.

Now, as far as the particular claim that ID hypotheses are not and cannot be falsifiable (and by extension any notion or hypothesis of God-like activity isn’t falsifiable either), it’s clearly not true or modern sciences that actually detect ID wouldn’t be possible – like forensics, anthropology, and SETI. As previously noted for you, the ID-only hypothesis can be tested in a potentially falsifiable manner – quite easily. All you have to do to falsify the ID-only hypothesis is show how something else could more reasonably explain the phenomenon in question – and the ID-only hypothesis is neatly falsified.

For example, if you can find a mindless naturalistic mechanism that can reasonably explain the origin of a highly symmetrical granite cube, you would neatly falsify the hypothesis that only ID can explain the origin of the cube. Short of this, however, the ID-only hypothesis gains a great deal of predictive value based on the strong weight of evidence that is currently in hand. That is why it is possible to tell the difference between the most likely origin of such a granite cube vs. a snowflake or the like.

The same is true for the God-only hypothesis. As I’ve explained for you multiple times now, there are various levels of phenomena that require various levels of intelligence to explain. As higher and higher level phenomena require higher and higher levels of intelligence and creative power to explain, one eventually comes to a point where the level of required intelligence and creative power is so high that it cannot be readily distinguished from what one would normally attribute to a God or God-like being. It is for this reason that if you yourself saw someone you knew was dead and decaying in the grave, raised to life at the word of someone claiming to be God, even you would tend to believe this claim – and rightly so. That means, of course, that the detection of God-like creative power is rationally detectable, at least in theory, given the presentation of such evidence.

Philosophical naturalism, on the other hand, is not at all testable in a potentially falsifiable manner. It is not even theoretically possible to falsify a theory that is dependent upon evidence that you have yourself proposed will show up at some undetermined time in the future. It is therefore not a science or otherwise rational, but is on the same level as wishful thinking – just not helpful.


    As an aside, I have to also point out that the claims for the creative potential of the evolutionary mechanism presented on this particular “Rational Wiki” webpage are not backed up by demonstration or reasonable statistical analysis or workable genetic theories – at least not beyond very low levels of functional complexity. They’re nothing but just-so stories. I mean, why hasn’t James Tour been convinced by this stuff? Because, there’s simply no science here… as you would know if you did your own independent research into the potential and limits of the evolutionary mechanism. Their claims regarding “flagellar evolution” are a case in point when it comes to glossing over the details and not understanding the exponentially growing problem of finding novel beneficial sequences in the vastness of sequence space with each step up the ladder of functional complexity: Link

The Creator of Time
How long should you look for a mindless naturalistic mechanism to explain a highly symmetrical granite cube before it becomes obvious that such a mechanism will most likely never be discovered? – that intelligent design is by far the most likely reason for its existence regardless of when or where such a cube might be found? – even if found on an alien planet like Mars?

Suggesting, at this point, that a mindless mechanism must be the answer for the origin of our granite cube, and that one day such a mechanism will be discovered, is not science – but faith that is deliberately blind to the strong weight of evidence that is currently in hand which puts a clear statistical limit on what all known mindless mechanisms are able to achieve, or are ever likely to achieve this side of eternity, with the material of granite.

Likewise, any religion that is based on the same blind faith, faith that is directly opposed to the weight of empirical evidence that is currently in hand, is no more helpful or trustworthy than the religion of philosophical naturalism. Such a religion would be “effectively indistinguishable from atheism” (William Provine, 1987).

As with science and any helpful hypothesis or theory, any useful religion which aims to establish a solid hope in rational people must be based on the weight of evidence which establishes the credibility and predictive power of the religion. If God exists, He is the creator of rational thought and scientific investigation and would not give these reasoning powers to us if He expected us to “forgo their use” (Galileo, 1615) – particularly when searching for Him and His signature in the works of nature or the inspiration of texts claiming to be derived from Him.

The Creator of Time
Again, if you personally don’t know why I’m wrong, or why someone like James Tour, a renown synthetic chemist, is wrong, why are you arguing with me here? You personally don’t know why I’m wrong, but you’re sure someone else does? – by faith? That’s the best you have? How many times have I heard that one before? Come on now. Your position, as with certain religious fundamentalists, is based entirely on your blind faith in the correctness of the claims of others, not a personal understanding of the issues in play.

Now, this faith of yours is great for you, but completely unhelpful for me or anyone else who wishes to have a personal understanding based on a reasonable explanation (like James Tour for instance) – an explanation that goes beyond a had wave and an appeal to some authority figure(s) who have yet to come up with a reasonable explanation themselves and make Nobel Prize winners and synthetic chemists afraid to admit as much in public forum much less publish anything counter to the prevailing dogma of the day (Link). This is especially true for someone, like me, who has studied this topic in great detail for many years and who is in fact able to explain the clear limits of the evolutionary mechanism and precisely why, statistically, these limits exist at the lowest levels of functional complexity (Link).

I’m sorry, but your faith in the claims of scientists and your arguments from authority have no explanatory value and are therefore entirely unhelpful to me. As Carl Sagan once wrote: “One of the great commandments of science is, ‘Mistrust arguments from authority.’ … Too many such arguments have proved too painfully wrong. Authorities must prove their contentions like everybody else.” (Link).

Why not at least try to figure it out for yourself? – see if you can understand it in a way that allows you to explain it to others who at least have a background in and basic understanding of biology and genetics?

“You see I get the design argument…”

How is that? How do you “get” the design argument when it comes to the origin or diversity of living things? – or even non-living things? You’re not even able to admit a clear difference between the origin of snowflakes and highly symmetrical granite cubes. You actually believe that the evolutionary mechanism is viable and that the arguments for abiogenesis are at least plausible and that the fine tuned features of the universe are at least theoretically explainable via the multiverse concept. Why? Because of some personal understanding of the topics? No. Because of your blind faith in the claims of popular scientists – that’s it. Otherwise, you evidently have no real understanding as to what you’re talking about when it comes to the creative potential and/or limitations of the evolutionary mechanism – or any other possible mindless naturalistic mechanism to explain the origin of life or of the universe itself. You also claim that it’s absolutely “impossible” to produce the modern biodiversity of land animals in just a few thousand years, starting from what could fit on an Ark, but you evidently have absolutely no personal understanding as to why (even though I’ve given you some pretty good hints as to why it is possible).

“but miracles, prophets, Santa Claus, fairies, ghosts, goblins, arks and the like are not proper subjects for science in my opinion.”

Perhaps that’s because you don’t understand how science works? Consider, for example, that the existence of gravity was detectable before anyone had any idea as to how gravity actually works. You see, knowing how something exists isn’t required for you to know that it exists. This means, of course, that if, theoretically, Santa Claus, fairies, ghosts, goblins, or prophets or miracles in general, of any kind, where to actually exist in the empirical world, then science, or any rational person for that matter, would in fact be able to detect such things if and when something were to happen outside of what mindless natural mechanisms could themselves explain (after a detailed investigation of course). It is only when mindless naturalistic mechanisms can reasonably explain a particular phenomenon that the “miraculous” would not be clearly recognizable to the rational person behind that particular phenomenon. If, for instance, one has no more evidence for their god than for the “celestial teapot” or the “spaghetti monster”, then there’s no good reason to believe in that god.

In short, then, as previously pointed out, science is not limited in its ability to detect the existence of the miraculous, if it ever theoretically occurred, but only in its ability to explain the miraculous…

I ask you, again, if you personally saw someone raised from the dead, whom you knew for sure was dead and rotting in the grave, you still wouldn’t believe what you saw with your own eyes? Of course you would believe it and so would everyone else, even scientists – despite an inability to explain how it happened. You see, its just not reasonable to claim that scientists or otherwise rational people are unable to even detect the miraculous – even if it were to theoretically occur (even if they were to see it with their own eyes and touch and examine it with their own hands). You’re clearly mistaken here…

Remember also that the assumption that future discoveries will one day be able to explain everything via mindless naturalistic mechanisms is not science, but a philosophy of naturalism that is very similar to a blind faith religion.

Academic Freedom Strikes Again!
No one actually believes that intelligent design is not rationally detectable behind various artifacts and phenomena that are clearly the result of deliberate design and intelligent intent. It is only in an effort to avoid acknowledging “God” that secular scientists who have taken on philosophical naturalism put forth superhuman effort to avoid admitting what is otherwise obvious.

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