Scientific articles that argue directly or indirectly for intelligent design, and irreducible complexity

Scientific articles that argue directly or indirectly for intelligent design, and irreducible complexity

https://reasonandscience.catsboard.com/t1498-scientific-articles-that-argue-directly-or-indirectly-for-intelligent-design-and-irreducible-complexity

Universality in intermediary metabolism Eric Smith and Harold J. Morowitz  September 7, 2004
The irreducible complexity of genetics-first origin scenarios is high, requiring joint emergence of catalysis, compartmentation, and heritability to make the minimal self-perpetuating structures.
https://www.pnas.org/content/101/36/13168

A functional skeletal system requires the COORDINATED DEVELOPMENT of many different tissue types, including cartilage, bones, joints, and tendons. 1

Koonin, the logic of chance, page 376
Breaking the evolution of the translation system into incremental steps, each associated with a biologically plausible selective advantage, is extremely difficult even within a speculative scheme let alone experimentally.

The cell is the irreducible, minimal unit of life 5
https://sci-hub.st/https://link.springer.com/chapter/10.1007/978-3-319-56372-5_8

Chemistry and the Missing Era of Evolution: A. Graham Cairns-Smith
We can see that at the time of the common ancestor, this system must already have been fixed in its essentials, probably through a critical interdependence of subsystems. (Roughly speaking in a domain in which everything has come to depend on everything else nothing can be easily changed, and our central biochemistry is very much like that.
https://sci-hub.ren/https://www.ncbi.nlm.nih.gov/pubmed/18260066

chemist Wilhelm Huck, professor at Radboud University Nijmegen
A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity
https://sixdaysblog.com/2013/07/06/protocells-may-have-formed-in-a-salty-soup/


Interdependency and phosphorylation of KIF4 and condensin I are essential for organization of chromosome scaffold
17 Aug 2017
Kinesin family member 4 (KIF4) and condensins I and II are essential chromosomal proteins for chromosome organization by locating primarily to the chromosome scaffold. However, the mechanism of how KIF4 and condensins localize to the chromosome scaffold is poorly understood. Here, we demonstrate a close relationship between the chromosome localization of KIF4 and condensin I, but not condensin II, and show that KIF4 and condensin I assist each other for stable scaffold formation by forming a stable complex. Moreover, phosphorylation of KIF4 and condensin I by Aurora B and polo-like kinase 1 (Plk1) is important for KIF4 and condensin I localization to the chromosome. Aurora B activity facilitates the targeting of KIF4 and condensin I to the chromosome, whereas Plk1 activity promotes the dissociation of these proteins from the chromosome. Thus, the interdependency between KIF4 and condensin I, and their phosphorylation states play important roles in chromosome scaffold organization during mitosis.

In this study, we further examined the interdependency of KIF4 and other scaffold proteins in chromosome organization. The results reveal that KIF4 localization to the chromosome scaffold is regulated interdependently with condensin I. The results indicate an interdependency of localization of KIF4 and condensin I on the chromosome scaffold.

It has been shown that condensin I loading to the chromosome is largely regulated by Aurora B [22–25]. This modification of condensin I is found to be conserved from yeast to humans [25]. Interdependency and physical interaction between KIF4 and condensin I for their chromosome localization raise the question whether KIF4 is regulated by Aurora B. In this study, interdependency and physical interaction between KIF4 and condensin I for localization to the chromosome were revealed. These results suggest that the interaction between KIF4 and condensin I may assist both proteins to bind and organize stably to the chromosome scaffold.




http://www.christianscientific.org/refereed-scientific-article-on-dna-argues-for-irreducibly-complexity/

http://www.evolutionnews.org/2013/10/paper_irreducib077761.html

e/10.1007%2Fs00018-013-1394-1


Scott Minnich at U. Idaho sends this along:

This paper published online his summer is a true mind-blower showing the irreducible organizational complexity (author’s description) of DNA analog and digital information, that genes are not arbitrarily positioned on the chromosome etc.

The paper by Muskhelishvili and Travers, titled “Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information”, makes several very interesting points. First, the digital information of individual genes (semantics) is dependent on the the intergenic regions (as we know) which is like analog information (syntax). Both types of information are co-dependent and self-referential but you can’t get syntax from semantics. As the authors state, “thus the holistic approach assumes self-referentiality (completeness of the contained information and full consistency of the the different codes) as an irreducible organizational complexity of the genetic regulation system of any cell”. In short, the linear DNA sequence contains both types of information. Second, the paper links local DNA structure, to domains, to the overall chromosome configuration as a dynamic system keying off the metabolic signals of the cell. This implies that the position and organization of genes on the chromosome is not arbitrary—much like Karl Drlica proposed years ago as we were obtaining the first bacterial genome sequences. In other words, DNA topology (due to supercoiling and histone-like protein binding), Transcription, and Metabolic energy (ATP levels influence DNA gyrase activity, which affects supercoiling, which affects transcription) are all keying off each other and thus there is an overall order to the positioning of anabolic and catabolic genes relative to the origin of replication. In short, I think this is a fascinating review looking at DNA organization and function which, in the authors words, are irreducibly complex.

http://link.springer.com/article/10.1007%2Fs00018-013-1394-1

Understanding genetic regulation is a problem of fundamental importance. Recent studies have made it increasingly evident that, whereas the cellular genetic regulation system embodies multiple disparate elements engaged in numerous interactions, the central issue is the genuine function of the DNA molecule as information carrier. Compelling evidence suggests that the DNA, in addition to the digital information of the linear genetic code (the semantics), encodes equally important continuous, or analog, information that specifies the structural dynamics and configuration (the syntax) of the polymer. These two DNA information types are intrinsically coupled in the primary sequence organisation, and this coupling is directly relevant to regulation of the genetic function. In this review, we emphasise the critical need of holistic integration of the DNA information as a prerequisite for understanding the organisational complexity of the genetic regulation system.

1. http://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/10208739

A new paper in the journal Cellular and Molecular Life Sciences, "Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information," argues that cellular mechanisms involved in processing genetic information make up an irreducibly complex system. The system requires genetic information, genetic machinery keyed to read that genetic information, as well as specific chromosomal organization. All of these components are necessary for what the paper calls "the organisational complexity of the genetic regulation system."
To be precise, the paper uses the term "irreducible organization" but it amounts to the same thing as biochemist Michael Behe's "irreducible complexity," and points implicitly to the same challenge to Darwinian accounts of origins.
The paper aims to critique the reductionist "Jacob-Monod paradigm," which fails to appreciate the complexity of genetic information, as well as the interaction between transcription factors and their target genes. Of course we're all familiar with genetic information in DNA being required to produce proteins. But the paper argues that in addition to the "digital information" in the primary DNA sequence, there is also "analog information" in the three-dimensional structure of chromosomes:

Recent studies have made it increasingly evident that the primary sequence of DNA in addition to the linear genetic code also provides three-dimensional information by means of spatially ordered supercoil structures relevant to all DNA transactions, including transcriptional control. In this review, we adopt the previously introduced terms "analog" and "digital" with regard to the two logically distinct types of information provided by the DNA. ... [A]ny DNA gene is a carrier of digital information by virtue of its unique base sequence. Moreover, a gene conceived as an isolated piece of linear code (no matter whether this isolation occurs at the level of transcription or posttranscriptional processing), is a discontinuous entity that can be expressed or not, thus principally consistent with an "on-or-off" logic and, therefore, belonging to digital information type. Conversely, the physicochemical properties of DNA, as exemplified by supercoiling and mechanical stiffness, are determined not by individual base pairs but by the additive interactions of successive base steps. Supercoiling is by definition a continuous parameter ranging between positive and negative values (you can have more or less of it), and so belongs to analog information type.

On top of the various forms of information in DNA, chromosomal structure is vital for gene regulation, as it helps control the interaction between transcription factors (TFs) that initiate transcription of their target genes (TGs):

several studies have proposed that the organisation of chromosomal structure on the evolutionary time scale is largely determined by the need of spatial optimisation of TF-TG interactions.

The paper then argues that the system of genetic regulation in cells is characterized by "irreducible organization":

Genetic regulation is crucial not only for sustaining the self-reproduction of a cell but also for substituting its worn-out constituents. This implies that a genetic regulation system, as a system consisting of physical elements, must be able not only to perform its primary function but also to perceive any internal changes of state so that it retains the potential, for example, to replenish its own components. In other words, it has to be self-referential. This peculiarity of organisation becomes conspicuous when compared to information coding in natural language, the syntactic and semantic properties of which provide logically different types of information. Syntax determines the structure of the rules of language and, thus, the way in which the words are assembled in sentences, whereas semantics determine the meaning of the words and so the available vocabulary. However, the structural rules of language cannot determine the meanings of the words, and nor is the vocabulary determinative for the structural rules of the language (we do not concern ourselves with any generative mechanisms relevant to the formal language theory here). Therefore, viewed as a coding system composed of two non-convertible types of information, natural language is not self-referential. By the same token, the Jacob-Monod paradigm separating the gene regulatory context from the genetic information is at variance with self-referential organisation. Notably, we do not use this term in the sense of elaborated mathematical concepts of distinction, circulation, feedback, re-entry, recursion, etc. Self-referential organisation, as we put it here, implies inter-conversion of information between logically distinct coding systems specifying each other reciprocally. Thus, the holistic approach assumes selfreferentiality (completeness of the contained information and full consistency of the different codes) as an irreducible organisational complexity of the genetic regulation system of any cell. Put another way, this implies that the structural dynamics of the chromosome must be fully convertible into its genetic expression and vice versa. Since the DNA is an essential carrier of genetic information, the fundamental question is how this self-referential organisation is encoded in the sequence of the DNA polymer.

The article even specifies that there are "Three basic components underlying the irreducible organisational complexity of any living cell" where "the organisation is essentially circular with all three basic components standing in relationship to reciprocal determination." Those three components are specified as transcriptional machinery, DNA topology, and metabolic energy. The authors are perplexed by how the "irreducible" and "circular" organization of this system arose since they admit, "we face a 'chicken or egg' dilemma -- on the one hand the TF-TG interactions are determinative for the chromosomal structure, and on the other hand this very same structure determines the regulatory interactions."
As noted, the paper recognizes that there are other types of information in DNA beyond merely the sequence of bases. What's incredible is that even though these two types of information are specified through different physical means, they nonetheless interact to regulate gene expression. The article explains that the supercoiling structure of DNA is vital to regulating gene expression, and at the same time it's not specified by the base-pair sequence. However, the base-pair sequence does interact with the supercoiling, and is more prone to localized untwisting to allow transcription:

In general, the regions of chromosomes that are sites for topological manipulation (such as, e.g., transcription and replication initiation sites) correlate strongly with low base stacking energies and high flexibility. Indeed, the sequences at the start sites of transcription and replication are prone to localised untwisting, whereas the termination sites -- and especially the regions between two converging translocases (be it a replisome or RNA polymerase) -- appear to easily adopt a writhed configuration acting as supercoil repositories. The emerging view is that manipulation of superhelical density and regulation of partitioning between twist and writhe is a fundamental property of both.

There are other levels of organization that have to do with the location and shape of the chromosome in time and space:

spatiotemporal integration of the analog (syntactic) and digital (semantic) properties of the chromosomal DNA code appears as a basic device coordinating the bacterial growth program. This coordination is facilitated by organising genes in a highly conserved order and orientation...

The article concludes: "chromosomes act as machines in which coordinated topological transitions operating at local (e.g. transcription initiation sites), regional (constrained superhelical domains) and global (entire chromosomes) levels specify the genetic activity."
All of this is pretty technical, but a summary sent to me by a pro-ID biologist helps explain how all of these difference levels of information are coordinated with one-another to facilitate basic cellular functions:

The authors describe the supercoiling (superhelicity) of the DNA, which affects levels of transcription in a rheostatic (analog) manner, is arranged in a gradient from the origin of replication to the terminus. Anabolic functions, which are expressed early in the cell cycle, show a preference to be on the leading strand (with regard to replication) and are organized close to the origin of replication, whereas catabolic functions are expressed late in the cell cycle, organized toward the terminal region of replication. Furthermore, the anabolic genes require high negative superhelicity for transcription, which is increased during rapid growth and therefore rapid replication of the DNA. So, during rapid growth, when anabolic functions become a limiting factor, a bottleneck if you will, the DNA replication generates more strain on the chromosome, i.e. more negative superhelicity, which is exactly the parameters for increasing anabolic functions. Brilliant.

How did these various independent levels of information become "coordinated"? Brilliance seems the best explanation for something brilliant.


http://www.evolutionnews.org/2013/10/paper_irreducib077761.html

Cryptic Genetic Variation Can Make “Irreducible Complexity” a Common Mode of Adaptation in Sexual Populations 1

Observe the first sentence in the first paper......which describes the problem : The existence of complex (multiple-step) genetic adaptations that are ‘irreducible’ (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard genetics parlance, these adaptations require the crossing of a wide adaptive valley of deleterious intermediate stages. And here the apparent falsification : Here we demonstrate, using a simple model, that evolution can cross wide valleys to produce ‘irreducibly complex’ adaptations by making use of previously cryptic mutations. When revealed by an evolutionary capacitor, previously cryptic mutants have higher initial frequencies than do new mutations, bringing them closer to a valley-crossing saddle in allele frequency space. Moreover, simple combinatorics imply an enormous number of candidate combinations exist within available cryptic genetic variation. We model the dynamics of crossing of a wide adaptive valley after a capacitance event using both numerical simulations and analytical approximations. Although individual valley crossing events become less likely as valleys widen, by taking the combinatorics of genotype space into account, we see that revealing cryptic variation can cause the frequent evolution of complex adaptations.

The reducible complexity of a mitochondrial molecular machine 2

Molecular machines drive essential biological processes, with the component parts of these machines each contributing a partial function or structural element. Mitochondria are organelles of eukaryotic cells, and depend for their biogenesis on a set of molecular machines for protein transport. How these molecular machines evolved is a fundamental question. Mitochondria were derived from an α-proteobacterial endosymbiont, and we identified in α-proteobacteria the component parts of a mitochondrial protein transport machine. In bacteria, the components are found in the inner membrane, topologically equivalent to the mitochondrial proteins. Although the bacterial proteins function in simple assemblies, relatively little mutation would be required to convert them to function as a protein transport machine. This analysis of protein transport provides a blueprint for the evolution of cellular machinery in general.

Behe's response:

http://behe.uncommondescent.com/2009/09/reducible-complexity-in-pnas/

Evolution versus "intelligent design": comparing the topology of protein-protein interaction networks to the Internet 3

Recent research efforts have made available genome-wide, high-throughput protein-protein interaction (PPI) maps for several model organisms. This has enabled the systematic analysis of PPI networks, which has become one of the primary challenges for the system biology community. In this study, we attempt to understand better the topological structure of PPI networks by comparing them against man-made communication networks, and more specifically, the Internet. Our comparative study is based on a comprehensive set of graph metrics. Our results exhibit an interesting dichotomy. On the one hand, both networks share several macroscopic properties such as scale-free and small-world properties. On the other hand, the two networks exhibit significant topological differences, such as the cliqueishness of the highest degree nodes. We attribute these differences to the distinct design principles and constraints that both networks are assumed to satisfy. We speculate that the evolutionary constraints that favor the survivability and diversification are behind the building process of PPI networks, whereas the leading force in shaping the Internet topology is a decentralized optimization process geared towards efficient node communication.

1) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4258170/
2) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747197/
3) http://www.ncbi.nlm.nih.gov/pubmed/17369648

http://www.pnas.org/content/113/2/316.abstract