Science Literature

The premier computer tool for simulating evolutionary processes has the name Avida. Researchers have reported studies on the evolution of complexity, altruism, changes to genetic architecture, and even the evolution of sex. Avida can be used to illustrate numerous concepts and mechanisms of Darwinian evolution and it has achieved a reputation as a platform for carrying out evolution experiments with digital organisms. As someone who has used simulation as a research tool, the question I have always asked (but to which I have struggled to find a satisfactory answer) concerns validation. It appears that Avida authors have made little or no attempt to cross-validate digital evolution with biological evolution. They have not attempted to move out of their virtual reality world by drawing attention to empirical experiments that give credibility to their conclusions. So how does Avida relate to the real world? At last, a paper has appeared which appears to ask similar questions:

" . . . some may ask whether the results of experiments with digital organisms have any relevance to living systems. We conclude that digital genetics is a valid platform for studying some biological questions, but that the applicability of results will depend critically upon the parameters used." (p.11)

The Avida Digital Life Platform demonstrates Darwinian concepts - but does it relate to the real world? (source here)

Inevitably, all simulation models have simplified the system being investigated. This is not, in itself, a problem as long as validation work is undertaken to establish what features in the simulated system can be mapped against the real-world system. So, for example, "key terms such as nucleotide, gene, heritability, selection, and fertility lack a clear equivalent in the software" (p.8). This can be OK, but users must not imagine an equivalence when none exists. Validation work to establish application areas is therefore both relevant and essential.

One problem with Avida has been the high values assigned to beneficial mutation rates and fitness effects.

"Previous experiments using Avida have studied the evolutionary emergence of complex features resulting from high-impact beneficial mutations. Avida's default settings provide mutational fitness effects of 1.0-31.0 for beneficial mutations that give rise to certain computational operations [. . .]. However, fitness effects this large are extremely rare in nature." (p.3)

Avida is constructed according to the Darwinian paradigm. The software is designed so that variations appear using mechanisms of mutation and natural selection. Avida assigns a high proportion of the digital genome to functionless code. Just as Darwinists imagine happens in the real world, so Avida has a genome much of which can be disturbed without disrupting fitness, but which is also capable of experiencing mutations that result in functionality. We now know that this is not a valid representation of the real world. The authors indicate that 85% of the Avida genome is initially benign, but it has the potential to contrinbute to fitness after certain mutations occur. However, as more and more functions are found for junk DNA, this aspect of Avida's design appears increasingly anachronistic.

"Mutations randomly substitute, insert, or delete single instructions in an Avidian genome, drawing upon 26 available instructions defined in the software. The ancestral genome devotes about 15 instructions to the essential replication code, while the remaining 85 positions are occupied by benign no-operation instructions, analogous to inert "junk DNA" that can be used as raw material for evolutionary tinkering." (p.3)

Although the software has been developed with Darwinian mechanisms in mind, the use of more realistic parameters needs attention - principally fitness effects and the proportion of advantageous mutations. The results reported by the authors do not confirm that Darwinian mechanisms can deliver the transformations that Darwinists claim. The problem with gradual incremental evolution is that small advantages are not selected naturally and do not become dominant in the population. Avida assumes and implements a scheme in which complex features can be built step-wise. Whether this is true for biological organisms is another question entirely.

"We observed that, when fitness effects in Avida are small, all advantageous logic operations are lost. Though digital organisms are peculiar in that they can survive such a loss, these data confirm that the accumulation of slightly deleterious mutations can lead to decreasing biological functionality and potentially eventual extinction. Because deleterious mutations are much more common than advantageous mutations in most systems studied, reduction in the efficacy of selection imposes strong directionality on evolution by favoring the fixation of deleterious mutations. The conditions under which fitness recovery may be possible should be studied more thoroughly using computational approaches." (p.12)

The most far-reaching conclusion relates to adaptation. "Plausible" adaptation accounts are pervasive in the literature of Darwinism (see here and here) but few of them are supported by empirical evidence. The Avida findings imply that "plausible" only means "realistic" when mutational fitness effects are large. With only marginal benefits, it is far more likely that "plausible" scenarios turn into "adaptationist just-so-stories".

"In contrast to Avida's default settings, most mutations in biological organisms are low-impact, and this class of mutations may dominate evolutionary change. When Avida is used with more realistic mutational fitness effects, it demonstrates a clear selection threshold. Mutations that influence fitness by approximately 20% or less come to be dominated by random genetic drift. Mutations that affect fitness by 7.5 - 10.0% or less are entirely invisible to selection in this system. These results provide evidence that low-impact mutations can present a substantial barrier to progressive evolution by natural selection. Understanding mutation is of primary importance, as selection depends on the mutational production of new genotypes. Numerous changes that would be beneficial may nevertheless fail to occur because mutation cannot produce them in the time available. Further, it is important for biologists to realistically appraise what selection can and cannot do under various circumstances. Selection may neither be necessary nor sufficient to explain numerous genomic or cellular features of complex organisms." (p.13)

It is worth considering how this research might affect the way evolutionary theory is presented in schools and universities. Adaptation is typically demonstrated by standard examples: peppered moths, Galapagos finches, antibiotic resistance, and more. The logic then appears to be: adaptive change is a real phenomenon so we can proceed on the basis that Darwinian evolution is validated, i.e. it is a plausible explanation for not just some but all features of life. This Avida research allows teachers and students to evaluate this questionable logic and assess the significance of these evidences.
* Are mutations low-, medium- or high-impact?
* What are the evidences relevant to random genetic drift?
* What data are relevant to assessing the relative proportions of low-, medium- and high-impact mutations?
* How important is the concept of "selection threshold" in evaluating potential evolutionary scenarios?
* Does the accumulation of low-impact mutations constitute a health hazard?

At the very least, students can be alerted to the fact that whilst examples of adaptation are documented in the literature, they occur only when mutational fitness effects are large enough. It follows that barriers to adaptive change may be just as important for understanding ecosystems as adaptation. This will take many out of their comfort zone (see here), but they can be encouraged by the thought that they are studying real science, not a virtual reality world.

The effects of low-impact mutations in digital organisms
Chase W. Nelson and John C. Sanford
Theoretical Biology and Medical Modelling, 2011, 8:9 | doi:10.1186/1742-4682-8-9

Abstract:
Background: Avida is a computer program that performs evolution experiments with digital organisms. Previous work has used the program to study the evolutionary origin of complex features, namely logic operations, but has consistently used extremely large mutational fitness effects. The present study uses Avida to better understand the role of low-impact mutations in evolution.
Results: When mutational fitness effects were approximately 0.075 or less, no new logic operations evolved, and those that had previously evolved were lost. When fitness effects were approximately 0.2, only half of the operations evolved, reflecting a threshold for selection breakdown. In contrast, when Avida's default fitness effects were used, all operations routinely evolved to high frequencies and fitness increased by an average of 20 million in only 10,000 generations.
Conclusions: Avidian organisms evolve new logic operations only when mutations producing them are assigned high-impact fitness effects. Furthermore, purifying selection cannot protect operations with low-impact benefits from mutational deterioration. These results suggest that selection breaks down for low-impact mutations below a certain fitness effect, the selection threshold. Experiments using biologically relevant parameter settings show the tendency for increasing genetic load to lead to loss of biological functionality. An understanding of such genetic deterioration is relevant to human disease, and may be applicable to the control of pathogens by use of lethal mutagenesis.

See also:

Anderson, E. Bits, Bytes and Biology: What Evolutionary Algorithms (Don't) Teach Us About Biology, ISCID Paper, November 2, 2004.

Truman, R. Evaluation of neo-Darwinian Theory with Avida Simulations (Part 1 and Part 2), PCID, 3(1), November 2004.

The essay stimulating this blog emerged from the Darwin Bicentennial year, when surveys of "educated lay people" in Switzerland revealed that only 20% had any clarity of thinking about Darwin's theory of evolution. About half explained it in a circular way, another 20% implied some form of Lamarckism and the remaining 10% talked about evolution being a flow towards complexity. These responses evidence "poor understanding" and two major reasons are suggested to explain the observations. The first is "The theory of evolution is counterintuitive" and the second is "The theory of evolution opposes most people's worldview". The worldview issues are of considerable importance to the issues considered here. It is worth asking: what is a Darwinian worldview? and why do most people have a different worldview? The first paragraph of the essay is significant for its candour:

"Early teaching of the basic principles of science by qualified teachers, together with the creative involvement of scientists, will help the general public to appreciate what the theory of evolution calls for, namely a worldview based on reality rather than on mysticism and dogma."

Worldviews affect the way we perceive and understand the world (source here)

OK, so Jacques Dubochet, the author of the essay, is linking Darwinism to a worldview based on reality and most of the general public, even those that are educated, have worldviews based on mysticism and dogma. At least this tells us where he's coming from. But Dubochet's reality is not self-evident. Indeed, many aspects of it are "shocking" because this reality conflicts with any worldviews that find a place for purpose and meaning transcending the individual level. As an example, Dubochet says that "the idea that our legs are not made for walking or our eyes for seeing is difficult to grasp". He recognises that most educated people do think our legs are made for walking and that our eyes are made for seeing - but considers these views to be delusional. These people need to be informed by Darwinism which shows us that "life evolves without a goal".

"The confrontation between intuitive understanding and reality is nothing new. The Copernican idea that the Earth revolves, not the Sun, also caused serious trouble in the past but nowadays everybody accepts it as obvious. Will this be the case with the theory of evolution? I have my doubts."

These doubts are interesting. Why is education not the answer? This brings us to the importance of worldview thinking. Dubochet does not dwell on the Copernican Revolution, but it is instructive. The intellectual world at that time was dominated by Aristotelianism. This had been integrated within Roman Catholicism by the influence of Thomas Aquinas - and the theologians happily went along with the views of their Aristotelian astronomers and interpreted the Bible accordingly. This became the Medieval worldview. The opposition to Copernicanism was led by the astronomers, who were sure that Aristotelian physics equated with reality. Outside the Catholic Church, it was possible for people to be more free-thinking and many of the early champions of Copernicanism were in the Reformation tradition. This led to a willingness to revisit biblical interpretation and they found that the relevant texts used the language of appearance and were not making scientific statements. For more on this, go here. At that time, if the education strategy had been followed, all that would have emerged would have been more and more complexities in the Ptolemaic system. What was really needed was an atmosphere where there was academic freedom and a willingness to critique alternative explanations of the data. This is what the Reformation facilitated and this is the culture that nurtured the rise of science.

Dubochet develops his worldview argument by saying that science answers "How?" questions and philosophy answers "Why?" questions. How-questions, he says, are concerned with causality and the quest to understand natural phenomena. Why-questions, however, imply goals, meaning and purpose. But Dubochet has already explained that Darwinism declares there is no goal and no "finality". To many of us, this seems as though Darwinism wants to claim the right to answer both "How?" and "Why?" questions!

"Why? What for? For which goal? For these questions, Darwin has an answer: in life, there is no finality, so the question "why" makes no sense, full stop! Here is where the shoe pinches. During discussions with non-specialists, signs of tensions are frequently observed the instant they understand that biological evolution does not lead anywhere."

It is at this point that Dubochet acknowledges that people have goals - but he only acknowledges that these goals are personal to individuals: "Humans have their future in their hands". Not only can we choose to inject meaning and purpose into our lives, we can clothe this desire for finality to include the adoption of religiosity.

"The human desire for finality extends further; it includes transcendance. Religiosity is, in fact, one more trait of our human nature as is made evident by ethnology, evolutionary biology, population genetics, or the science of religion. Where does this come from? It has been suggested that it offers a sufficient advantage to be selected by evolution. Others think it is a necessary corollary to the development of human intelligence when faced with the fear of death. Still others see religion as a by-product of some other naturally selected function. In all cases, the consequence for us is that "Some form of religious thinking seems to be the path of least resistance for our cognitive systems.""

So, not only do Darwinists make claims about "Why?" questions, they also seek to understand religion and human psychology from Darwinian perspective. On these grounds, they will allow religious life to coexist with the Darwinian view of reality. As an example, the "blameless Darwinian" in the following quote is Francis Collins, a leading US theistic evolutionist Christian.

"Even if the theory of evolution describes life without involving divine action, it does not prove the absence of transcendence or the non-existence of God. The blameless Darwinians who declared their indisputable religiosity prove that a peaceful collaboration is possible. In my view, it should be valued."

If anyone is in any doubt, this form of religiosity is far removed from biblical Christianity. Instead of subjective goals, the Christian maintains a cosmic purpose that integrates all history. Instead of an existential choice to secure meaning, the Christian affirms God's plan to be the master plan for all. Eyes are made for seeing and ears are made for hearing (for more, go here). Divine action is everywhere, for "in him we live and move and have our being". This is a different worldview from that described by Dubochet.

The main take-home message from this blog is that there is such a thing as a Darwinian worldview, that those adhering to this view consider themselves to be living in the real world and all others have succumbed to mysticism and/or dogma. This post should be read in parallel with "Creationism and Intelligent Design in science lessons" which argues for treating Darwinism as a worldview at all levels of education. The following quote comes from the conclusion of that blog:

"Darwinism does not exist in isolation from a worldview and the attempt by many to portray it as objective 'pure' science is philosophically naive. Just as the objections of creationists and ID scholars cannot be properly understood without a worldview perspective, so also the commitments of evolutionary biologists to the blind watchmaker model of evolutionary transformation cannot be properly understood without reference to the worldview of these scientists."

As an example of what the Darwinian worldview entails, and why educationalists should be alert to the metaphysical implications of Darwin's theory, Dubochet's essay is necessary reading. Worldviews affect the way all of us perceive the world. The Darwinian view is no exception. It has to deny the truth claims of Christianity. If coexistence with religion is envisaged, it must be based on privatised religious commitments that are ultimately superstition and delusion - nothing to do with ultimate truth. It is not surprising (or shocking) when Darwinists say these things - knowing their worldview, such words are entirely predictable.

Our response should be that of the scientists in the Reformation tradition: let us question dogmas, test hypotheses, perform relevant experiments and follow the evidence wherever it leads. What we seem to be getting from many Darwinians is a hardening attitude that presumes that only they live in the real world. Consequently, humanist champions of evolution are seeking changes to education policy that will deny academic freedom to both students and teachers with a different worldview. Their stance is one that has to be resisted.

Why is it so difficult to accept Darwin's theory of evolution?
Jacques Dubochet
Bioessays, 33: 240-242, April 2011 | DOI 10.1002/bies.201000142

Most educated people do not understand Darwin's theory of evolution. This is because the idea that our legs are not made for walking or our eyes for seeing is difficult to grasp. Adepts of intelligent design have it easier. Furthermore, stating that life evolves without a goal and in the absence of finality is shocking for most people because it clashes with their idea of the meaning of life. In fact, the theory of evolution is intellectually satisfying and it can serve as a solid basis for a responsible worldview in the sense of the Enlightenment. It need not come into conflict with transcendental belief. Early teaching of the basic principles of science by qualified teachers, together with the creative involvement of scientists, will help the general public to appreciate what the theory of evolution calls for, namely a worldview based on reality rather than on mysticism and dogma.

Michael Reiss deserves credit for his persistence in advocating views that are counter to those of many individuals and organisations. The issues are concerned with the way evolutionary theory is taught in schools. There is, and should continue to be, an evaluation of alternative approaches and the arguments presented by Reiss in his recent scholarly paper deserve a fair hearing.

"I am especially interested in the education provided to those for whom education is mandatory. I am also concerned to make suggestions that can be implemented in today's classrooms. [. . .] I concentrate on the UK, though argue that in fact there are fewer differences between countries in this regard than is commonly suspected." (p.401)

Handling controversy in the classroom need not be stressful (source here)

In developing his approach, Reiss considers whether creationism and intelligent design (ID) are "controversial" issues. This has relevance because educationalists have a long tradition of teaching about controversies. They do not fear that the mere exposure of students to a controversial issue will undermine all the foundations that have been previously laid. The inference is that if creationism and ID are deemed controversial issues, then any good science teacher will take this as an opportunity to develop a scientific mind and use the controversies to advantage. However, as Reiss notes, "What is controversial for one group may not be controversial for another." There are evolutionary scientists who do not regard creationism and ID as controversial - for them, this issue is settled. The continuing phenomenon of creationism and ID is regarded by them as a subversive anti-science tendency in society. Similarly, there are creationists who present evolutionary theory "as illogical [. . .] contradicted by the scientific evidence, [. . .] the product of non-scientific reasoning." Since both groups use rational arguments to make their case, Reiss seeks to understand the issues within a broader philosophical framework.

"As is generally accepted, there are two major epistemological families for knowledge that is not a priori: those centred on perceiving the world for ourself, and those centred on the testimony of others. There is obviously not the space here to go into a major discussion of each of these but it is sufficient for my purposes to note that in both cases knowledge, for all that it may be reliable, has an element of provisionality. Of course, some knowledge is more provisional than others. A useful distinction in science is made by Imre Lakatos who argued that scientists work within research programmes. A research programme consists of a set of core beliefs surrounded by layers of less central beliefs. Scientists are willing to accept changes in these more peripheral beliefs so long as the core beliefs can be retained." (p.402)

This brings us to the topic of worldviews, which is increasing in importance in science education. Reiss quotes approvingly a definition by Aerts et al. (1994): "A worldview is a coherent collection of concepts and theorems that must allow us to construct a global image of the world, and in this way to understand as many elements of our experience as possible" (p.405). The question is being asked: 'Is science itself a worldview?'

"The term has recently been explored as a way of helping conceptualise why, despite the best efforts of many science educators, so few students leave their schooling with the sort of scientific understanding and disposition that most science teachers wish they had. The principal conclusion is that school science fails to enable most students to see the world from a scientific perspective." (p.405)

To illustrate the relevance and importance of worldviews, Reiss turns to the film "March of the Penguins". This has been the most successful nature film in America motion picture history and it has received several awards. A contributory factor was the endorsement of the "Christian right". Reviewers in this tradition found the film to be a compelling message of love, perseverance and God's intelligent design. All this was communicated rationally by the reviewers, revealing how the worldview of the Christian "right" found meaning, purpose and intelligent design revealed in the natural world. Perspective is vitally important, so much so that it highlights the "difficulty of using the criterion of 'reason' to decide whether an issue is controversial or not." It also suggests that "standard ways of addressing the diversity of student views in a science classroom may be inadequate." (p.407)

Reiss goes on to articulate what he means by the phrase "standard ways". In the UK, the Department of Children, Schools and Families produced "Guidance on creationism and Intelligent Design" - rejecting the idea that creationism and ID can be considered science. The report suggested that the only context for referring to these issues is to explain why they are not to be "considered to be scientific theories" and why evolution "is considered to be a scientific theory". In the US, the National Academy of Science guidance says much the same.

Why are these approaches inadequate? Reiss cites one analysis that suggests the guidance looks like placing "a gag order on teachers" and fails to engage meaningfully with children and communities of people who find creationism and ID thinking persuasive. Reiss refers also to Thomas Nagel, who finds that the "so-called scientific reasons for excluding ID from science lessons do not stand up to critical scrutiny". (For a related post, go here). Furthermore, the UK guidance for considering these issues in religious education units is quite different in character from the guidance previously mentioned: the RE guidelines encourage teachers to give students opportunities to explore the issues. Additionally, Reiss points out that much of the discourse on creation, ID and evolution overlooks primary school contexts:

"I should note that the distinction between science lessons, religious education lessons and citizenship lessons, while it may hold at secondary level with subject-specific teaching rather breaks down at primary level where a pupil generally has the same teacher for most or all lessons. From an epistemological point of view this is both the strength and potential weakness of primary teaching. Teaching in the primary school has the potential to make links between subjects with greater ease than is generally the case at secondary school, precisely because the one teacher is responsible for such a diversity of subjects." (p.410)

Reiss is advocating a change of stance about the way creationism and ID are handled in science lessons. Instead of going into battle over controversies, Reiss advises a discourse that is sensitive to worldviews.

"An advantage of shifting the discourse from controversy to sensitivity is that one shifts the focus from epistemology to pedagogy. One can be sensitive with someone in respect of an issue without implying that one shares the same perspective (or worldview) as the person to whom one is being respectful and considerate." (p.411)

Most of Reiss' analysis is very helpful and good common sense. Adopting his approach will enhance the educational experience of all pupils. However, there is one major area where I would like to see a further development of the analysis: this is to provide a more thorough analysis of science using a worldview perspective. What should we make of Reiss when he writes: "The scientific worldview is materialistic in the sense that it is neither idealistic nor admits of non-physical explanations" (p.403)? Some of us do not find this summary one that we would use in our scientific work. In fact, the prohibition of non-physical explanations should be regarded as an example of the way many modern scientists are idealistic, bringing to science a precondition about what the natural world ought to be like and how it ought to behave. This is particularly relevant to the origin of information - materialistic science has to interpret information in terms of random variations that are selected and fixed. Consequently, they have no tools to test whether the approach is realistic or can be falsified - as a matter of ideology, it cannot be falsified!

Science is not neutral territory for scholarship. Ideologies, presuppositions, paradigms and worldviews are important for all branches of science, including evolutionary biology. Darwinism does not exist in isolation from a worldview and the attempt by many to portray it as objective 'pure' science is philosophically naive. Just as the objections of creationists and ID scholars cannot be properly understood without a worldview perspective, so also the commitments of evolutionary biologists to the blind watchmaker model of evolutionary transformation cannot be properly understood without reference to the worldview of these scientists. Then it will be clear that many of their key concepts (the Tree of Life emerging from a single cell, common descent, the central role of variation and natural selection) go far beyond what can reasonably be inferred from the data and ultimately are derived from the worldview of the evolutionist.

Using this approach with students will avoid labelling any group as having a "non-scientific worldview". Rather students will be more aware of the role of presuppositions and ideologies in science, will be able to understand better why scientific revolutions occur, and will be better equipped to understand why science thrives in some cultures more than in others. Instead of the controversy about Science & Faith, students will be aware of the way personal belief systems feed into and influence the way science is practiced. This seems to me to be far healthier for science than the present grid-locked polemics.

How should creationism and intelligent design be dealt with in the classroom?
Michael J. Reiss
Journal of Philosophy of Education, 45(3), August 2011, 399-415 | DOI: 10.1111/j.1467-9752.2011.00790.x

Abstract: Until recently, little attention has been paid in the school classroom to creationism and almost none to intelligent design. However, creationism and possibly intelligent design appear to be on the increase and there are indications that there are more countries in which schools are becoming battle-grounds over them. I begin by examining whether creationism and intelligent design are controversial issues, drawing on Robert Dearden's epistemic criterion of the controversial and more recent responses to and defences of this. I then examine whether the notion of 'worldviews' in the context of creationism is a useful one by considering the film March of the Penguins. I conclude that the 'worldviews' perspective on creationism is useful for two reasons: first it indicates the difficulty of using the criterion of reason to decide whether an issue is controversial or not; secondly, it suggests that standard ways of addressing the diversity of student views in a science classroom may be inadequate. I close by examining the implications of this view for teaching in science lessons and elsewhere, for example in religious education lessons and citizenship lessons and at primary level where subject divisions cannot be made in so clear-cut a manner.

See also:

Tyler, D. Science education and the origins issue (ARN Literature blog, 3 June 2011)