By Ann Gauger
Here are links to the published articles all in one place, in case you missed something.
You will notice certain themes recur:
- Evolutionary algorithms succeed only because of active information.
- The origin of new protein folds and new protein functions continues to cause a problem for evolution.
- The organizational and information-bearing properties of the genetic code are not explained by Darwinian processes.
- Old ideas in biology— anthropocentrism, structuralism and second law problems—gain a fresh hearing.
And new ideas are advanced:
- Design in biology is as much about what isn’t done as what is done.
- The sequence-structure-function relationship found in biology—
where a linear DNA code translates to a 3D protein, which in turn
produces a biological function— has an analogy in human language, namely
Chinese ideograms. With the proper tweaking this analogy can be
exploited to test what random changes to code (that writes Han
characters) does to the functional product. Enter Stylus, a
computational model for testing evolution.
The links are live, so go explore.
2013
Active Information in Metabiology Winston Ewert, William A. Dembski, Robert J. Marks II
The Types: A Persistent Structuralist Challenge to Darwinian Pan-Selectionism Michael J. Denton
The Place of Life and Man in Nature: Defending the Anthropocentric Thesis Michael J. Denton
Entropy and Evolution Granville Sewell
2012
A Tetrahedral Representation of the Genetic Code Emphasizing Aspects of Symmetry Fernando Castro-Chavez
Climbing the Steiner Tree—Sources of Active Information in a Genetic Algorithm for Solving the Euclidean Steiner Tree Problem Winston Ewert, William A. Dembski, Robert J. Marks II
Lignin—Designed Randomness Matti Leisola, Ossi Pastinen, Douglas D. Axe
Time and Information in Evolution Winston Ewert, William A. Dembski, Ann K. Gauger, Robert J. Marks II
2011
A Stylus-Generated Artificial Genome with Analogy to Minimal Bacterial Genomes Douglas D. Axe, Philip Lu, Stephanie Flatau
The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway Ann K. Gauger, Douglas D. Axe
Can the Origin of the Genetic Code Be Explained by Direct RNA Templating? Stephen C. Meyer, Paul A. Nelson
2010
The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations Douglas D. Axe
A Vivisection of the ev Computer Organism: Identifying Sources of Active Information George Montañez, Winston Ewert, William A. Dembski, Robert J. Marks II
Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness Ann K. Gauger, Stephanie Ebnet, Pamela F. Fahey, Ralph Seelke
The Case Against a Darwinian Origin of Protein Folds Douglas D. Axe
By Ann Gauger
The most recent article published in BIO-Complexity considers
the wild and abstruse world of metabiology, a theoretical computational
attempt to model evolutionary biology. Dr. Gregory Chaitin began the
work in 2009, and it has progressed to the point described in his 2012
book Proving Darwin, shown below. The question is, does his model succeed?
Winston Ewert, William Dembski and Robert Marks II take on that question in their article in BIO-Complexity, whose abstract is below. I will let them speak for themselves.
Active Information in Metabiology
Winston Ewert, William A. Dembski, Robert J. Marks II
Abstract
Metabiology is a fascinating intellectual romp in the surreal world
of the mathematics of algorithmic information theory. In this world,
halting oracles hunt for busy beaver numbers and busy beaver numbers
unearth Chaitin’s number, knowledge of which in turn allows resolution
of numerous unsolved mathematical problems, many of whose solutions
would earn large cash bounties. All this, despite the fact that halting
oracles can’t be implemented on a computer, a computer can never make a
list of busy beaver numbers, and Chaitin’s number, always a positive
real number less than one, is proven to be unknowable. The fun of
metabiology is the application of these ideas to illustrate Darwinian
evolution. When metabiology’s evolutionary process is stripped of the
glitter of algorithmic information theory, however, what remains is a
procedure similar to that used in other attempts to model Darwinian
evolution, like the ev and AVIDA computer programs. Metabiology, like ev
and AVIDA, succeeds because available sources of knowledge about the
solution being sought can be mined. We show the mining of information
from a halting oracle has striking similarities to mining information
from a simple Hamming oracle. Unlike a halting oracle, however, Hamming
oracles can be implemented on a computer. We demonstrate that for both
oracles, information can be mined by search strategies that are
analogous in some respects even though the methods differ; in both cases
the search strategy used greatly influences the result. Because
metabiology’s process relies on unknowable numbers and infinite
resources, its reported relative performance measures can only be
expressed asymptotically. That is, the results of metabiology are only
proven to be true on the largest possible scale. In fact, simple
simulations using bounded resources suggest the asymptote is not always
approached quickly, indicating that metabiology results may only hold
for scales larger than any practical system.
By Ann Gauger
Entropy and Evolution
The second law of thermodynamics sounds imposing, but the idea is
simple. It was originally framed in terms of thermal entropy, and
can be stated thus: In a closed system, entropy tends to increase.
That means, in a closed system where there are local hot and cold
spots, eventually the whole system will reach a state where everything
is the same temperature.
The second Law also has been used to explain the tendency of all
things to go from order to disorder. Left unattended, things break down.
And conversely, things don’t spontaneously organize themselves into
complex structures unless they are receiving input from somewhere. Think
about 747 jets for example. You can wait a thousand million years and a
jet will not assemble itself from parts, even if a tornado blows
through. But try it the other way—put a jet on a tarmac in Kansas and
wait a thousand years, and you will see entropy at work, even without
the tornado.
The second Law has been used as an argument against unguided
evolution: life cannot spontaneously self-assemble without input
from the outside, because such a striking increase in order violates the
second Law. The rebuttal usually comes by saying that the planet Earth
is not a closed system, because it receives energy from the sun.
How to unweave this brangle? In the recent paper from BIO-Complexity,
the mathematician Granville Sewell takes on the topic in a way that
should be accessible to most. If you want to find out how he handles tornados, you will have to read the paper!
Read More
By Ann Gauger
Michael Denton is the author of our third article in the
continuing series on research and critical review articles published in
BIO-Complexity in 2013. Here Denton addresses the question, “Are there
laws of form (or Types) in biology? And what is their source?” The idea
that there are underlying rules that govern biological structures, rules
that cannot be explained by natural selection, is very old, and
pre-dates Darwinism. He presents the classical reasons for the idea of
Structuralism, and explains how Pan-selectionism, the belief that
natural selection can explain everything in biology, came to dominate
biologists’s thinking. He then describes how recent research is tipping
things back the other way.
Abstract pattern is ubiquitous throughout the living realm. This
image of radiolarian shells is taken from Plate 31 of Ernst
Haeckel’s Kunstformen der Natur (Artforms of Nature),1904.
The Types: A Persistent Structuralist Challenge
to Darwinian Pan-Selectionism
Michael J. Denton1,2 *
1Aditya Jyot Eye Hospital, Mumbai, INDIA
2Discovery Institute, Seattle, Washington, USA
Abstract
Here I first review the structuralist or typological
world view of pre-1859 biology, and the concept that the basic forms
of the natural world—the Types—are immanent in nature, and
determined by a set of special natural biological laws, the so-called
‘laws of form’. I show that this conception was not based, as Darwinists
often claim, on a priori philosophical belief in Platonic
concepts, but rather upon the empirical finding that a vast amount of
biological complexity, including the deep homologies which define
the taxa of the natural system, appears to be of an abstract,
non-adaptive nature that is sometimes of a strikingly numerical and
geometric character. In addition, these Types exhibit an extraordinary
robustness and stability, having in many instances remained
invariant in diverse lineages for hundreds of millions of years. Second,
I show that neither Darwinism nor any subsequent functionalist
theory has ever provided a convincing adaptive or
functionalist explanation for the Types or deep homologies. Third, I
discuss how recent advances have provided new support for
the structuralist notion that the basic forms of life are immanent
in nature. These include the discovery of the cosmic fine tuning of
the laws of nature for life as it exists on earth, and advances in
areas of molecular and cellular biology, where it is apparent that a
considerable amount of biological complexity is clearly determined by
the self-organizing properties of particular categories of matter,
rather than being specified in detail in a genetic blueprint as
functionalism demands.
Denton MJ (2013) The Types: A persistent structuralist challenge
to Darwinian pan-selectionism. BIO-Complexity 2013 (3):1−18. doi:10.5048/BIO-C.2013.3
By Ann Gauger
Smithsonian/Flicker http://flic.kr/p/5tRFwT
From the paper by Michael Denton, called “The place of life and man in nature: Defending the anthropocentric hypothesis”:
"The question of questions for mankind—the problem which underlies
all others, and is more deeply interesting than any other—is the
ascertainment of the place which mankind occupies in nature and of his
relations to the universe of things."
– Thomas Huxley, Man’s Place in Nature
For centuries the traditional teleological anthropocentric framework
provided the answer to Thomas Huxley’s “question of questions.” But
following the Copernican revolution and particularly after the
publication of Darwin’s On the Origin of Species,
the traditional framework was seen to be increasingly untenable;
mankind, so it seemed, had no special place in nature. However, as I
show, discoveries in chemistry and biochemistry in the 19th and
early 20th centuries, and in cosmology and fundamental physics and
comparative physiology during the course of the 20th century,
have reopened the ‘grand debate’ by providing intriguing new
support for the old and seemingly obsolete anthropocentric paradigm.
By Ann Gauger
In our second article in the series we present a paper by Michael Denton, who is well known for his seminal work Evolution: A Theory in Crisis.
Here he lays out arguments from physiology and biochemistry to show
that the behaviors of basic chemical molecules like oxygen, water, and
carbon dioxide are uniquely suited for living beings like
ourselves.
The Place of Life and Man in Nature: Defending the Anthropocentric Thesis
Michael J. Denton
Abstract
Here I review the claim that the order of nature is uniquely suitable
for life as it exists on earth (Terran life), and specifically for
living beings similar to modern humans. I reassess Henderson’s
claim from The Fitness of the Environment that the ensemble of
core biochemicals that make up Terran life possess a unique
synergistic fitness for the assembly of the complex chemical systems
characteristic of life. I show that Henderson’s analysis is still
remarkably consistent with the facts one century after it was written.
It is still widely accepted even among researchers in astrobiology.
I also review the evidence for believing that many of the
properties of the same core set of biochemicals are specifically
fit for the physiology of complex terrestrial beings resembling
modern humans. I show that none of the recent advances in the field
of extremophile biology, alternative biochemistries, or recent
allusions to apparent defects in the fitness of nature for Terran
life significantly undermine the core argument, that nature is
peculiarly fit for carbon-based Terran life, and especially for the
physiology of complex terrestrial beings resembling modern humans.
Denton MJ (2013) The place of life and man in nature: Defending the anthropocentric thesis. BIO-Complexity 2013 (1):1–15.
doi:10.5048/BIO-C.2013.1
By Ann Gauger
We are beginning a series highlighting work published this year in the on-line journal BIO-Complexity.
All articles are freely accessible, and address questions relevant to
intelligent design theory from a variety of points of view. This first
critiques a theoretical construct called metabiology that seeks to demonstrate evolution by using algorithmic information theory.
Active Information in Metabiology
Winston Ewert,1* William A. Dembski,2 Robert J. Marks II1
1Electrical & Computer Engineering, Baylor University, Waco, Texas, USA
2Discovery Institute, Seattle, Washington, USA
Abstract
Metabiology is a fascinating intellectual romp in the
surreal world of the mathematics of algorithmic information theory. In
this world, halting oracles hunt for busy beaver numbers and busy
beaver numbers unearth Chaitin’s number, knowledge of which in turn
allows resolution of numerous unsolved mathematical problems, many of
whose solutions would earn large cash bounties. All this, despite
the fact that halting oracles can’t be implemented on a computer, a
computer can never make a list of busy beaver numbers, and
Chaitin’s number, always a positive real number less than one, is proven
to be unknowable. The fun of metabiology is the application of
these ideas to illustrate Darwinian evolution. When metabiology’s
evolutionary process is stripped of the glitter of algorithmic
information theory, however, what remains is a procedure similar to that
used in other attempts to model Darwinian evolution, like
the ev and AVIDA computer programs. Metabiology, like ev and
AVIDA, succeeds because available sources of knowledge about the
solution being sought can be mined. We show the mining of information
from
a halting oracle has striking similarities to mining information from a
simple Hamming oracle. Unlike a halting oracle, however, Hamming
oracles can be implemented on a computer. We demonstrate that for both
oracles, information can be mined by search strategies that are
analogous in some respects even though the methods differ; in both cases
the search strategy used greatly influences the result. Because
metabiology’s process relies on unknowable numbers and infinite
resources, its reported relative performance measures can only be
expressed asymptotically. That is, the results of metabiology are
only proven to be true on the largest possible scale. In fact,
simple simulations using bounded resources suggest the asymptote
is not always approached quickly, indicating that metabiology
results may only hold for scales larger than any practical system.
Ewert W, Dembski WA, Marks II RJ (2013) Time and information in evolution. BIO-Complexity 2013 (4):1–19. doi:10.5048/BIO-C.2013.4
By Ann Gauger
I really like the candidness of the essay by Rajendrani Mukhopadhyayover at the American Society for Biochemistry and Molecular Biology published in October.
It starts by acknowledging that researchers really don’t know how
sophisticated structures like the modern protein shown above ever arose.
As one researcher put it:
“Once you have identified an enzyme that has some weak, promiscuous
activity for your target reaction, it’s fairly clear that, if you have
mutations at random, you can select and improve this activity by several
orders of magnitude,” says Dan Tawfik at
the Weizmann Institute in Israel. “What we lack is a hypothesis for the
earlier stages, where you don’t have this spectrum of enzymatic
activities, active sites and folds from which selection can identify
starting points. Evolution has this catch-22: Nothing evolves unless it already exists.” (Emphasis added).
The article then goes on to discuss why the problem is so hard,
making a tour of prominent researchers’ opinions about ways to escape
the catch-22 described above. It’s all pretty hypothetical, and relies
on circumstances and conditions not now in evidence. Hmmm.
Perhaps the author of the essay, and Dr. Tawfik, have their doubts too. The article closes with :
Overall, what the field of protein evolution needs are some
plausible, solid hypotheses to explain how random sequences of amino
acids turned into the sophisticated entities that we recognize today as
proteins. Until that happens, the phenomenon of the rise of proteins
will remain, as Tawfik says, “something like close to a miracle.”
Yup.
