Saturday, March 11, 2006
Book Review by Massimo Pigliucci (Nature Magazine)
There have been rumblings for some time to the effect that the neo-darwinian synthesis of the early twentieth century is incomplete and due for a major revision. In the past decade, several authors have written books to articulate this feeling and to begin the move towards a second synthesis. In the past decade, several authors have written books to articulate this feeling...
...I framed the debate in terms of the integration of development, environment and genetics by articulating the concept of "developmental reaction norms"...
...Jablonka and Lamb provide a framework that includes not one but four sources of inheritance in living organisms: there is the standard genetic one, based on nucleic acids such as DNA and RNA; there are epigenetic inheritance systems, such as (but not limited to) chromatin marking systems and RNA-interference systems for gene silencing; third, there are behavioural inheritance systems, including behaviour- influencing substances (think pheromones) and social learning (both imitative and not); finally, humans have also developed a symbolic inheritance system based on the ability to communicate by manipulating symbols...
...The authors argue that there is more to heredity than genes; that some hereditary variations are non-random in origin; that some acquired information is inherited; and that evolutionary change can result from 'instruction' as well as selection. This may sound rather revolutionary, even preposterously close to lamarckism. But Jablonka and Lamb build on evidence from standard research in evolutionary and molecular biology, and their case should be examined on its merits, rather than being dismissed by a knee-jerk reaction...
...The clamour to revise neo-darwinism is becoming so loud that hopefully most practising evolutionary biologists will begin to pay attention. It has been said that science often makes progress not because people change their minds, but because the old ones die off and the new generation is more open to novel ideas. I therefore recommend this and the other books I mentioned on the future of evolutionary theory to the current crop of graduate students, postdocs and young assistant professors. They'll know what to do.
[Gilbert & Sarkar, Developmental Dynamics, Sept '00]
Organicism (materialistic holism) has provided the philosophical underpinnings for embryology since the time of Kant. It had influenced the founders of developmental mechanics, and the importance of organicism to embryology was explicitly recognized by such figures as O. Hertwig, H. Spemann, R. Harrison, A. M. Dalq, J. Needham, and C. H. Waddington. Many of the principles of organicism remain in contemporary developmental biology, but they are rarely defined as such. A combination of genetic reductionism and the adoption of holism by unscientific communities has led to the devaluation of organicism as a fruitful heuristic for research. This essay attempts to define organicism, provide a brief history of its importance to experimental embryology, outline some sociologically based reasons for its decline, and document its value in contemporary developmental biology. Based on principles or organicism, developmental biology should become a science of emerging complexity. However, this does mean that some of us will have to learn calculus. [Evolution]
Friday, March 10, 2006
[Gilbert, Int. J. Dev. Biol. 47: 467-477 (2003)]
The early studies of evolutionary developmental biology (Evo-Devo) come from several sources. Tributaries flowing into Evo-Devo came from such disciplines as embryology, developmental genetics, evolutionary biology, ecology, paleontology, systematics, medical embryology and mathematical modeling. This essay will trace one of the major pathways, that from evolutionary embryology to Evo-Devo and it will show the interactions of this pathway with two other sources of Evo-Devo: ecological developmental biology and medical developmental biology. Together, these three fields are forming a more inclusive evolutionary developmental biology that is revitalizing and providing answers to old and important questions involving the formation of biodiversity on Earth. The phenotype of Evo-Devo is limited by internal constraints on what could be known given the methods and equipment of the time and it has been framed by external factors that include both academic and global politics. [Evolution]technorati tags: evolution, evo-devo, biology, ecology, genetics, paleontology, systematics, biodiversity
Thursday, March 09, 2006
[Shapiro, Boston Review, Mar '97]
"The recent reviews in your columns of books by Dennett, Dawkins, and
Behe are testimony to the unflagging interest in controversies about
evolution. Although such purists as Dennett and Dawkins repeatedly
assert that the scientific issues surrounding evolution are basically
solved by conventional neo-Darwinism, the ongoing public fascination
reveals a deeper wisdom. There are far more unresolved questions than
answers about evolutionary processes, and contemporary science
continues to provide us with new conceptual possibilities.
Unfortunately, readers of Boston Review may remain unaware of this
intellectual ferment because the debate about evolution continues to
assume the quality of an abstract and philosophical "dialogue of the
deaf" between Creationists and Darwinists. Although our knowledge of
the molecular details of biological organization is undergoing a
revolutionary expansion, open-minded discussions of the impact of
these discoveries are all too rare. The possibility of a non-
Darwinian, scientific theory of evolution is virtually never
considered. In my comments, then, I propose to sketch some
developments in contemporary life science that suggest shortcomings
in orthodox evolutionary theory and open the door to very different
ways of formulating questions about the evolutionary process. After a
discussion of technical advances in our views about genome
organization and the mechanisms of genetic change, I will focus on a
growing convergence between biology and information science which
offers the potential for scientific investigation of possible
intelligent cellular action in evolution."
Wednesday, March 08, 2006
Heylighen F. (2000): "Evolutionary Transitions: how do levels of complexity emerge?", Complexity 6 (1), p. 53-57-- A joint review of 5 books (by Pettersson, Maynard Smith & Szathmary, Coren, Stewart and Turchin) discussing the evolution of complexity levels.
It is a common observation that complex systems have a nested or hierarchical structure: they consist of subsystems, which themselves consist of subsystems, and so on, until the simplest components we know, elementary particles. It is also generally accepted that the simpler, smaller components appeared before the more complex, composite systems. Thus, evolution tends to produce more complex systems, gradually adding more levels to the hierarchy. For example, elementary particles evolved subsequently into atoms, molecules, cells, multicellular organisms, and societies of organisms. These discrete steps, characterized by the emergence of a higher level of complexity, may be called "evolutionary transitions". The logic behind this sequential complexification appears obvious: you can only build a higher order system from simpler systems after these building blocks have evolved themselves. The issue becomes more complicated when you start looking for the precise mechanisms behind these evolutionary transitions, and try to understand which levels have appeared at what moment, and why.
In recent years, several authors have tried to tackle this issue. As we will see, their approaches are diverse, and their results are concomitantly different. Part of the reason for this incoherence is that these researchers have worked mostly in isolation: they come from different traditions, and their works hardly make reference to each other. This is understandable, since the emergence of hierarchical levels is a pre-eminently multidisciplinary issue, involving at least physics, chemistry, biology and sociology.
[Dembski, PCID, '04]
"Michael Behe's concept of irreducible complexity, and in particular his use of this concept to critique Darwinism, continues to come under heavy fire from the biological community. The problem with Behe, so Darwinists inform us, is that he has created a problem where there is no problem. Far from constituting an obstacle to the Darwinian mechanism of random variation and natural selection, irreducible complexity is thus supposed to be eminently explainable by this same mechanism. But is it really? It's been eight years since Behe introduced irreducible complexity in Darwin's Black Box - a book that continues to sell 15,000 copies per year in English alone (Amazon UK | US). I want in this essay to revisit Behe's concept of irreducible complexity and indicate why the problem he has raised is, if anything, still more vexing for Darwinism than when he first raised it. The first four sections of this essay review and extend material that I've treated elsewhere. The last section contains some novel material."
As promised in last night's Personal Post (Are Human Beings 'Irreducibly Complex'? A whimsical thought...) here is the caveat:
My perception of the concept [irreducible complexity] is similar to that of Pierre-Paul Grasse who believed 'Internal Factors' were involved in how evolutionary changes occurred - see Grasse, Behe, and "Irreducible Complexity". [John Latter]
Tuesday, March 07, 2006
University of Chicago study overturns conventional theory in evolution (Jun '05)
1) Press Release
New data suggest that the accumulation of genetic changes is not solely determined by natural selection. A study by University of Chicago researchers contradicts conventional theory by showing that the percentage of mutations accepted in evolution is also strongly swayed by the speed at which new mutations arrive at a gene: the faster the speed of new mutations, the greater the percentage of those mutations accepted.
"We've discovered a striking phenomenon that challenges a paradigm of molecular evolution that has been around for several decades," said lead author Bruce Lahn, Ph.D., assistant professor of genetics at the University of Chicago and Howard Hughes Medical Institute investigator. "As such, it may cause a significant shift in the field."
Full text at:
2) A highly unexpected strong correlation between fixation probability of nonsynonymous mutations and mutation rate.
[Wyckoff et al, Trends in Genetics, Jul '05]
Under prevailing theories, the nonsynonymous-to-synonymous substitution ratio (i.e. K(a)/K(s)), which measures the fixation probability of nonsynonymous mutations, is correlated with the strength of selection. In this article, we report that K(a)/K(s) is also strongly correlated with the mutation rate as measured by K(s), and that this correlation appears to have a similar magnitude as the correlation between K(a)/K(s) and selective strength. This finding cannot be reconciled with current theories. It suggests that we should re-evaluate the current paradigms of coding-sequence evolution, and that the wide use of K(a)/K(s) as a measure of selective strength needs reassessment.
Full text at:
Monday, March 06, 2006
Todays entry in the Personal Posts category briefly comments on why no attention will be given to "Cultural Evolution" other than that applicable to the third of the current Aims:
3) Address those cultural factors which are applicable to answering the question "If an internal evolutionary mechanism exists, then why hasn't it been found before?"John Latter
technorati tags: cultural+evolution
The Evolution of Life on the Earth: Scientific American Magazine; October 1994; by Gould
Some creators announce their inventions with grand eclat. God proclaimed, "Fiat lux," and then flooded his new universe with brightness. Others bring forth great discoveries in a modest guise, as did Charles Darwin in defining his new mechanism of evolutionary causality in 1859: "I have called this principle, by which each slight variation, if useful, is preserved, by the term Natural Selection."
Natural selection is an immensely powerful yet beautifully simple theory that has held up remarkably well, under intense and unrelenting scrutiny and testing, for 135 years. In essence, natural selection locates the mechanism of evolutionary change in a "struggle" among organisms for reproductive success, leading to improved fit of populations to changing environments. (Struggle is often a metaphorical description and need not be viewed as overt combat, guns blazing. Tactics for reproductive success include a variety of nonmartial activities such as earlier and more frequent mating or better cooperation with partners in raising offspring.) Natural selection is therefore a principle of local adaptation, not of general advance or progress.
Yet powerful though the principle may be, natural selection is not the only cause of evolutionary change (and may, in many cases, be overshadowed by other forces).
[This article is also available here]
Sunday, March 05, 2006
The first of the "Aims" referred to in yesterday's Main Blog post is:
1) To develop the model indicated by the 'anomalies' referred to in Why research an 'Internal Evolutionary Mechanism'? (1) - and hopefully avoid the pitfalls inherent in doing so!
Below is a description of the basic concept (warts and all) as it has appeared on my website since 1998:
The Post-Notochord Model
The diagram opposite shows a dotted area within which all internal and external "inputs" come together and it is here that an internal evolutionary mechanism is proposed to exist. Cannon (1929) formulated the concept of "homeostasis" whereby activity at this level can be described as "self regulating" or "automatic" which are observations of a closed system made from an external standpoint.
The model proposes, when viewed from the inside, any non thinking and non intelligent organism with such a configuration is simply maintaining equilibrium and that this equilibrium extends in another direction - that of evolution.
The dotted area, arbitrarily labeled the A.O.N.E. ("Area of Natural Equilibrium"), is a localized area at the apex (or center) of the internal homeostatic hierarchy [Note 1: The Triune Brain]. The genome in such an organism's germ cells, equally hierarchically integrated, will also have a localized area and this connectivity reflects the continuity of organism-genome-organism.
Changes in the life experiences of an organism as 'experienced' at the level of the AONE - not that of consciousness - may cause single or co-ordinated evolutionary/devolutionary changes to occur if existing thresholds are exceeded, or just as importantly, not met. These 'changes', transmitted to germ cells, would then cascade down (or radiate outwards) from their localized areas into the genome, and in a direction that would begin (or achieve) restoration of equilibrium in the next generation(s).
The following flowchart will be used to demonstrate how an homeostatic mechanism can accounts for various aspects of evolution:
To recap: The fibonacci series begins "0, 1, 1, 2 ,3, 5" and each subsequent number can be formed by adding the two preceeding numbers together, eg 2 + 3 = 5, 3 + 5 = 8, 5 + 8 = 13 (etc.).
If the larger of two sucessive fibonacci numbers is divided by the smaller then a number is obtained which increasingly approximates to the 'golden ratio' or 'golden number': 1.6180339887498948482....
The flowchart opposite will generate the fibonacci series endlessly.
For simplicity it ignores the first zero, and rather than 'seeding' the program and adding succesive fibonacci numbers together, it generates the numbers via testing the ratio of 'x over y' against phi (where phi equals the golden number/ratio).
'y' is the fibonacci number produced, 'x' the incremental count. 'F' is required to test whether the 'x over y' ratio is closer to the golden ratio when x/y is above or below it.
NB I hope the maths are correct - please email any comments (and I would like help/advice in developing this further).
The above two entries have been taken from existing material and will serve as an initial 'baseline'. I'll post ongoing development in the Persoanl Posts category and then here in the Main Blog when I'm happier with how things are going - correspondence over a recently reported phenomena, for example, gives an indication of how a mathematical model could be developed but also demonstrates just how basic the above is!
[Jablonka, Lamb, Avital, Trends in Ecology & Evolution, May '98]
Lamarckism and Darwinism are traditionally seen as alternative
theories trying to account for evolutionary change. The verdict of
history is that Lamarck got it wrong - evolutionary change does
not occur through the inheritance of acquired characters. Acquired
characters are the outcome of instructive processes, such as those
seen in embryonic induction, transcriptional regulation, and
learning all of which involve highly specific and usually adaptive
responses to factors external to the responding system. The
inheritance of the outcomes of instructive processes is deemed to
be impossible. Adaptive evolutionary change is assumed to be based
on darwinian (or more accurately neo-darwinian) evolution in which
guidance comes exclusively from selective processes. The
production and nature of heritable variation is assumed to be
uninformed by the environment or by previous history. The future
is open-ended, determined solely by the contingencies of life. lt
is neither foretold nor intimated.