Home » Intelligent Design » ISCID and ARN member Albert de Roos in 3 peer-reviewed journals

ISCID and ARN member Albert de Roos in 3 peer-reviewed journals

Albert de Roos is a long time participant at International Society of Complexity Information and Design and Access Research Network. de Roos is not formally an advocate of intelligent design theory but has been a friendly and valuable supporter of the dialogue. His papers argue that in order for evolution to proceed, evolution must proceed by applying software design principles such as “design-by-contract”.

His accepted papers are:

Conserved intron positions in ancient protein modules Biology Direct 2:7

Recently, it was reasoned based on the engineering paradigm design-by-contract, that exon concatenation of modular exonic sequences was the basis of eukaryotic genome formation

Origins of introns based on the definition of exon modules and their conserved interfaces. Bioinformatics. 2005, 21:2-9

ABSTRACT
Summary: Central to the unraveling of the early evolution of the genome is the origin and role of introns. The evolution of the genome can be characterized by a continuous expansion of functional modules that occurs without the interruption of existing processes. The design-by-contract methodology of software development offers a modular approach to design that seeks to increase flexibility by focusing on the design of constant interfaces between functional modules. Here, it is shown that design-by-contract can offer a framework for genome evolution.

and

The origin of the eukaryotic cell based on conservation of existing interfaces. Artif Life. 2006 Fall;12(4):513-23

5.5 Design by Contract as a Framework The new mechanism proposed here is based on an evolutionary model in which self-contained modules interact with each other by constant interfaces [14], a general method for reducing complexity and could give evolution the necessary robustness, flexibility, and extensibility. This design pattern is abstracted in the software development methodology known as design by contract [50] in which the interface is viewed as specifications of the mutual obligations, or contracts. The effect of constant interfaces across self-contained modules is a reduction of the interdependences across modules or components and a reduction of the risk that changes within one module will create unanticipated changes in other modules. The constancy of interfaces in evolution is enforced by the dependence of all downstream processes on an established interface. Self-assembly processes are by definition self-contained and they decrease complexity by reducing dependences on external factors. The proposed sequence of events during the acquisition of an exomembrane, including the export mechanism of ribosomal subunits, is in line with a model based on the conservation of existing interfaces during evolution. The evolutionary model of self-contained modules that interact with conserved interfaces can provide a general framework for the creation of artificial life.

His ideas have received a somewhat cool reception in the ID community probably because he thinks natural selection can function as a designer substitute. However, he articulates what design principles a designer might use in order to succeed at realizing a working design.

He correctly approaches the problem of identifying designs in biology by relating them to man-made engineering designs and design organizing principles. The search for analogues in biology to man-made engineering designs is the search for specified complexity in biology, and thus de Roos has provided an illustration how to use the Explanatory Filter in practice. de Roos is providing a model of how fruitful ID research could be profitably pursued.

The refutation of mindless OOL and Darwinism is moving forward quite well. The next step for ID research is to apply design detection (I prefer to use the phrase “design identification”) techniques so that our understanding of biology and opportunities for medical advancements can be made.

In addition, de Roos has made a very good critique of traditional models of cellular evolution (such as endosymbiosis and prokaryotes-first theories), and has thus advanced our knowledge in these areas. Furthermore, reverse engineering the software architecture of life by presuming a “design by contract” metaphor may prove a fruitful avenue of research. If one can reverse engineer the “contract” or requirements of an engineering design, one can understand the design far better, because to understand the purposes of a design is the a good step in understanding the design.

Some of his submitted papers are available at ISCID: Origin of insect metamorphosis based on design-by-contract: larval stages as an atavism

and

Evolution Based on Design-by-Contract: Origin of Life through an abiotic double-stranded RNA world

De Roos is listed in ResearchID. Congratulations Albert de Roos!

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5 Responses to ISCID and ARN member Albert de Roos in 3 peer-reviewed journals

  1. Here is something Albert wrote recently at ARN Creation science in the journal Science? :

    let’s first admit that mainstream evolutionary science is as teleological as creation science

  2. Thanks Sal for bringing my research to the attention of a larger audience.

    What I am trying to do is to apply design patterns that are used in engineering to evolution. We have to treat evolution as a molecular machine, and since all complex machines are based on a design, this would hold for evolution as well.

    I am in the process of publishing the article on the origin of life in Biology Direct as well, which will give some interesting insight in the different points of view I have on the OOL research. To one the comments (which Biology Direct publishes) of the reviewers I reply:

    “I think the efforts in trying to make a self-replicating ligase ribozyme may be a dead-end for explaining the evolution of life. The theoretical approach used in my article not only identifies alternative solutions, it also argues against scenarios that violate the used engineering rules. The incorporation of a dual function in one molecule will not provide the necessary flexibility for the individual evolution of the different functionalities. It seems impossible to move from a single-stranded genome to a double-stranded while maintaining functional continuity. A reliance on external independent systems would not be in line with a required self-contained character of a complex system as evolution. Thus, before focusing on making a self-replicating replicase, we should be sure that it leads to an explanation of Life where these problems are sufficiently addressed to form a coherent mechanistic series of events.”

    Soon I will be publishing more background of my views on albertderoos.nl

  3. You are more than welcome Albert, and even though you and I may have some differing views, it seems both of us accept that applying teleological metaphors to biology is the correct approach to understanding it.

    In addition to identifying a specific design, you have gone one step further and tried to identify design principles. “Design by Contract” is an attempt to identify some of the design principles in place. For example, energy efficiency, robustness, modifiability (the software term for evolvability), reusability (modularity) are all design principles.

    The goal of a Design Identification research program was outlined in the US Department of Energy:

    BRINGING THE GENOME TO LIFE

    In order to understand biological systems at this next level, we must engage the most advanced research talents and resources. The potential payoff is enormous: an understanding of the underlying concepts that have resulted from four billion years of evolutionary tinkering will provide tools to revolutionize the study of human health. Similarly, the design principles used by nature to evolve biological systems can be adapted for use by today’s engineers to develop a new generation of man-made biological machines tailored to carry out specific functions such as degrading foreign compounds or synthesizing new medicines.

    I maintain whether the designs were by Intelligence or whatever, they are identifiable via an Explanatory Filter as the Explanatory Filter is how we identify design in course of every day life.

    Thus, a scientist may view design and its appeal to a designer as simply a fruitful device for understanding the world, not attaching any significance to questions such as whether a theory of desig is in some ultimate sense true or whether the designer actually exists.

    William Dembski
    No Free Lunch, p. xv

    Though I may intensely disagree with some regarding the cause of ultimate origins, the use of teleological metaphors and the process of reverse engineering designs and design identification will be indispensible to understanding biology.

  4. [...] Albert de Roos explains, The difficult thing with the endosymbiotic theory is that it proposes no real mechanism and most textbooks show the simplistic picture of a cell that swallows another cell that becomes a mitochondrion. Unfortunately, it is not so simple as that. There is a difference between the process of endosymbiosis and its incorporation in the germline, necessitating genetic changes. What were those changes? What was the host? Was it a fusion, was it engulfment, how did the mitochondrion get its second membrane, how did two genomes in one cell integrate and coordinate? The theory is also strongly teleological, illustrated by the widely used term ‘enslavement’. But how do you enslave another cell, how do you replace its proteins and genes without affecting existing functions? The existence of obligate bacterial endosymbionts in some present eukaryotes is often presented as a substitute for a mechanism, but they remain bacteria and give not rise to new organelles. So, before we can speak of the endosymbiotic as a testable scientific theory, we need a mechanistic scenario which is lacking at the moment. [...]

  5. [...] Albert de Roos explains, The difficult thing with the endosymbiotic theory is that it proposes no real mechanism and most textbooks show the simplistic picture of a cell that swallows another cell that becomes a mitochondrion. Unfortunately, it is not so simple as that. There is a difference between the process of endosymbiosis and its incorporation in the germline, necessitating genetic changes. What were those changes? What was the host? Was it a fusion, was it engulfment, how did the mitochondrion get its second membrane, how did two genomes in one cell integrate and coordinate? The theory is also strongly teleological, illustrated by the widely used term ‘enslavement’. But how do you enslave another cell, how do you replace its proteins and genes without affecting existing functions? The existence of obligate bacterial endosymbionts in some present eukaryotes is often presented as a substitute for a mechanism, but they remain bacteria and give not rise to new organelles. So, before we can speak of the endosymbiotic as a testable scientific theory, we need a mechanistic scenario which is lacking at the moment. [...]

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