Intelligent Design

Things to consider when thinking about ID

Obviously, the genome and the cell’s information-processing and storage system manifest many features— hierarchical filing, nested coding of information, context dependence of lower-level informational modules, sophisticated strategies for increasing storage density, etc.  We would expect to find these feature if they were intelligently designed and intelligently integrated to function together with the least amount of duplication of effort and waste as possible.  On the other hand, many of these incredibly complex features that have been discovered are not easily explained by the standard materialistic evolutionary mechanisms. Amoebas to Atheists is just a giant leap of faith.


On top of that, these incredible informational features are found not only in the highest-level multi-cellular organisms but also in single-celled prokaryotes.  This suggests an intriguing, if radical, possibility.  It suggests that intelligent design may have played a role in the origination of complex multi-cellular organisms, and that mutation and selection, along with those other undirected mechanisms of evolutionary change, do not completely account for the origin of these higher forms of life.

Might intelligent design have played a role in biological evolution— that is, in the origin or historical development of new living forms from simpler pre-existing forms?  Given the importance of information to living systems, and given that all forms of life, including the most complex multi-cellular organisms, display distinctive hints and concepts of intelligent design in their informational systems, there would now seem to be an increasing reason to consider this possibility.

The neo-Darwinian perspective has limitations, which leaves a number of research questions not being addressed.  We now know that organisms contain information of different types at every organizational level in the cell, including ontogenetic or structural information not encoded in DNA.  According to neo-Darwinism, new form and structure arise as the result of information-generating mutations in DNA.  How to reconcile these difficulties has caused some form of linguistic gymnastics on the part of neo-Darwinian’s leading proponents.

Neo-Darwinism has long assumed in its population-genetics models of evolutionary change, a number of things about genes that we now (because of extensive scientific experimentation) know to be incorrect.  As an example, these models assume that: 1) genetic information is context-independent (a specific codon produces one effect only), 2) that genes independently associate (they migrate to each other to build the appropriate proteins),  and 3) that genes can mutate indefinitely with little regard to extragenomic and other functional constraints (which has been shown that one mutation can destroy the existing cell).

I wanted to get some images of the above concepts but they are none that really look good and explain the concepts well.  When we get to describing the concepts, it will make more sense and I will be able to use some of the images.

In short, neo-Darwinism gives dormancy to the gene as the focus of biological change and innovation.  By doing so, it assumes a one-dimensional conception of biological information.  This way neo-Darwinism provides little reason to consider or investigate (and every reason to ignore) the additional tiers of information and other codes that reside beyond the gene and all through the cell.  Whereas, advocates of intelligent design not only acknowledge, but also expect to find, sophisticated modes of information storage and processing in the cell.  The theory of intelligent design treats the hierarchical organization of information as theoretically significant; advocates of the theory have naturally shown intense interest in the cell’s informational hierarchies and intricate modes of coding fond throughout the interior and even the cell wall itself.

A design-theoretic perspective tends to encourage questions about the hierarchies of information in life that neo-Darwinists tend to (or prefer to) ignore. Questions you have probably never, ever thought about, but which are necessary to answer the mystery of the mystery.  Questions such as:

  • Where exactly does this ontogenetic[1] information reside?
  • How does it affect the function of lower-level genetic modules?
  • How many types of information are present in the cell?
  • What part do they play in maintaining the integrity and functioning of the cell?
  • How much ontogenetic information is present in the cell?
  • How do we measure this information, given that it is often structural and dynamic rather than digital and static?
  • In addition, how mutable are various forms of non-DNA-based information— if at all?

We know that animal body plans[2] are static over long periods of time. Once we have an animal with segmented body or multiply eyes that stay in the ‘evolutionary’ tree for a time.  Is this morphological stasis[3] the result of constraints imposed upon mutability by the interdependence of informational hierarchies?  If so, what are they?  Are there other constraints— even probabilistic constraints operating at the level of the individual gene and proteins— that limit the transformative power of the selection and mutation mechanism?  Given the phenomenon of “phenotypic plasticity[4]” (individuals in a population with the same genotype that have different phenotypes) and the recurrence of similar variations in the same species, how much variability in organisms is actually the result of preprogramming as opposed to random mutations?  If these variations continue to recur, are they the result of genetic preprogramming?  If so, then where does the requisite information for these programs reside and how is it expressed chemically within the cell?  How many phenomena currently regarded as examples of so-called neo-Lamarckian processes[5] can be properly attributed to preprogrammed, intelligently designed, adaptive capacity?  All these questions arise naturally from a design-theoretic perspective and have little place in a neo-Darwinian framework and they continue to mock them

Then we have questions about the structure, function, and composition of living systems themselves.  Some are questions about the efficacy of various evolutionary mechanisms— questions about whether these mechanisms can explain various appearances of design as well as an actual designing intelligence.  Can mutation and selection produce by random selection of mutational happenstance to produce new body parts and structures?  Can selection and mutation produce novel genes and proteins needed to keep these new parts or structures working?  If not, are there mechanisms or features of life that impose limits on biological change?  On the other hand, are there perhaps other materialistic mechanisms that have the causal powers to produce novel forms of life? Moreover, what kinds of causal powers would that be?  If not, and if the pervasive hallmarks of intelligent design in complex organisms indicate actual design, what does that imply about what else we should find in living systems or the fossil record?

You can see where the direction of this series is going by now I am sure.  Is the science of Intelligent Design equal to or superior than neo-Darwinian mutational natural selection?  Which theory best explains what we know and understand of the past.  Which theory best explains what microbiologists are currently discovering?  We will follow that direction in this series of articles.  I may slip in a Biblical verse now and then, but only to indicate that what we are currently discussing was foretold years ago.  I will not base any of the scientific facts on creationism- that is completely different from Intelligent Design (ID).

Are there patterns in the fossil record indicative of intelligent activity?  If so, do they suggest that intelligent design played a role in the production of novel body plans or smaller innovations in form?  Is intelligent design necessary to begin to build new forms of life that exemplify higher taxonomic categories— such as orders, classes, and phyla?  Could some form of design be needed to build the new forms encompassed by lower taxonomic categories such as genera and species?  How much morphological change can undirected mechanisms such as selection and mutation produce, and at what point, if any, would intelligent design be need to participate?

Such questions move from whether intelligence played a role in the history of life to when, where, and how often intelligence acted.  If intelligent design played a role in the history of life after life’s initial origin, did that designing agency act gradually or discretely?  If a designing intelligence generates new forms by infusing new information into the biosphere, do we see evidence of that anywhere in the geological time scale?  If so, where, and how can we detect it?  Did it affect a gradual transformation of form from simple to more complex organisms?  Alternatively, did that intelligence affect more sudden transformations or innovations in biological form, thus initiating new and separate lines of genealogical descent?

In other words, is the history of life monophyletic or polyphyletic?  If polyphyletic, how many separate lines of descent or trees of life have existed during life’s history.  Would that explain the gaps in the fossil record, embryological development, comparative anatomy, and phylogenetic studies in that case?  If life’s history is polyphyletic, how wide are the envelopes of variability in the separate trees of life? Does that explain the ridiculous numbe rof cladograms that overlap and distract from one another.  Conversely, if undirected evolutionary mechanisms are sufficient to account for the origin of all new forms of life, is it possible that the pervasive signs of design in higher forms of life were preprogrammed to unfold from the origin of life itself?  If design was thus “front-loaded” in the first simple cell, what does that imply about the capacity of cells to store information for future adaptations?  And what should the structure and organization of the prokaryotic genome look like in that case?

Many of the preceding questions follow from considering the informational signature of intelligence in life.  The DNA and RNA and the proteins folds and ATP motors all are incredibly complex and difficult to see how they could arise by mutation alone.  But design arguments from irreducible complexity, suggest other kinds of research questions. Are specific molecular machines irreducibly complex?  If so, is intelligent design the only cause known to produce this feature of systems?  How can evolution explain the origin of the flagellar motor and other molecular machines?  Indeed, the controversy irreducible complexity has already motivated specific new lines of empirical inquiry and generated a number of new research questions.  Many of the lines of inquiry are admittedly radical from an orthodox neo-Darwinian point of view, and some scientists may not want to consider them. Nevertheless, they cannot argue that the scientists who do will have nothing to do.


A Genus can contain multiple Species, as well as a Family contains many Genus etc on up the chain.  We will discuss this classification system later in more detail and show how it is useless to indicate how species are related to others.

While the first three articles and this one have been more or less simplified

The remaining articles will at least require a minimum of a high school education to understand.  I will do my best to write in such a way as to be understandable as possible.  Enjoy the series.  The next one is the DNA enigma, The molecular Labyrinth, the origin of science and design, chance and pattern recognition, playing the odds, and much more.

[1] the origination and development of an organism, usually from the time of fertilization of the egg to the organism’s mature form

[2] an assemblage of morphological features shared among many members of a phylum-level group.  This term, usually applied to animals, envisages a “blueprint” encompassing aspects such as symmetry, segmentation and limb disposition. Evolutionary developmental biology seeks to explain the origins of diverse body plans

[3] unchanging body type implying constancy with little change to the basic defining characters.

[4] the ability of an organism to change its phenotype in response to changes in the environment

[5] the idea that an organism can pass on characteristics that it has acquired during its lifetime to its offspring (also known as heritability of acquired characteristics or soft inheritance)


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