Science Literature

According to Massimo Pigliucci and Maarten Boudry, the widespread use of machine-information metaphors is unfortunate and misleading. They complain about textbooks that develop metaphors to a considerable level of detail. As an example, they cite Alberts, who is often quoted for his analogy between a cell and a "miniature factory, complete with assembly lines, messengers, transport vehicles, etc." Another machine metaphor they dislike is that of the genome as a "blueprint", notably in the hype surrounding the Human Genome Project. Whilst these analogies are widely held within the scientific community and by educators, the main target of Pigliucci and Boudry's paper appears to be intelligent design:

"The analogy between living organisms and man-made machines has proven a persuasive rhetorical tool of the ID movement. In fact, for all the technical lingo and mathematical 'demonstrations', in much of their public presentations it is clear that ID theorists actually expect the analogies to do the argumentative work for them. In Darwin's Black Box, Behe takes Alberts' machine analogy to its extreme, describing the living cell as a complicated factory containing cargo-delivery systems, scanner machines, transportation systems and a library full of blueprints."

From the Editorial of Molecular Cell (October 2010): "Looking at a textbook picture of a cell, it all seems perfectly serene within, like a bird's eye view of a beautiful city. Zooming in close, however, a much more dynamic image emerges (see the cover). It soon becomes apparent that cells encounter a wide variety of conditions, many of which can induce stresses. These insults must be carefully and appropriately dealt with to maintain the balance that is needed for cell survival and growth." (Source here)

Pigliucci and Boudry rightly trace the emergence of machine metaphors back to, at least, the Middle Ages, and a rise to prominence with the rise of science in the 17th Century. The well-known analogy made by William Harvey is mentioned: the human heart is a pump. The authors also rightly point out that the scientists of the time gave these metaphors some additional substance, because they considered human designs to be imaging designs of the Creator.

"For Newton and many of his contemporaries, the importance of the mechanical conception of nature was greater than the mere term 'metaphor' would suggest, as the development of mechanistic philosophy was itself largely inspired by religious motivations. As Shanks wrote in his account of the history of the design argument, "the very employment of machine metaphors invited theological speculation"."

The authors turn to David Hume to find arguments foreshadowing the demise of design inferences made by the science community. Hume's (1779) Dialogues concerning natural religion is said to expose "several problems with the central analogy". The key thought is that our experience of design is limited to human artifacts, and it is presumptuous to extrapolate from this and make statements about design in general and God's design in particular.

"Hume realized that, at least in some cases, appearances of intelligent design can be deceptive. [. . .] Although Hume does not deny that we can discern similarities between nature and human artifacts, he warns us that the analogy is also defective in several respects. And if the effects are not sufficiently similar, conclusions about similar causes are premature. [. . .] Aware of the fallibility and imperfections of human reasoning, Hume remains highly skeptical about the design inference and the machine analogy, even though he was not able to provide a satisfactory explanation for the appearance of design in nature."

It has always surprised me that David Hume's arguments are considered weighty. The preceding generations of scholars did have a rationale for thinking that there is a relationship between the Creator's design and human design. This was based on the concept of image-bearing, drawn from the Judeo-Christian worldview of the time. If man is made in the image of God, they reasoned, then we design because God designs, and analogies can be drawn between human design and design in nature. Science became, for Johannes Kepler as for them all, "thinking God's thoughts after him".

The real challenge came when the theistic worldview of the pioneers of science was replaced by the deistic worldview of the Enlightenment scholars and the naturalistic worldview of their heirs. Only then does Hume's argument become coherent - and even then, design inferences can still be made at the level of hypotheses that can be tested and potentially falsified.

However, Pigliucci and Boudry suggest these metaphors and analogies are bad science. This needs to be examined closely. They object to the 'cell as a factory' analogy, the 'genome as blueprint' analogy, the 'bacterial flagellum as rotary motor' analogy, and the 'biochemical processes as digital characters in a machine code' analogy. Significantly, all these examples relate primarily to our understanding of how cells function. The major objections to metaphors, however, are linked to theories of development and the need for a viable theory of evolutionary transformation. This gives the clue to the real argument of this paper: Pigliucci and Boudry want to show that the neodarwinian synthesis and genetic reductionism have failed to deliver answers to the real problems of development and evolution, and the popular 'genome as blueprint' metaphor is inhibiting the critical appraisal of existing theory.

The 'blueprint' metaphor receives extensive discussion. They say that wherever it is used, it is always in the context of molecular biology research, not the organism as a whole. They claim that many biologists are concerned about the "hyper-reductionist approach brought about by the molecular revolution". With new discoveries about gene regulation and epigenetics, the blueprint metaphor is looking increasingly limited in its application.

"[N]ew ways of thinking about development and evolution are building a conceptual vocabulary that increasingly distances itself from the machine-information metaphor. [. . .] An answer that is being explored successfully is the idea that the information that makes development possible is localized and sensitive (as well as reactive) to the conditions of the immediate surroundings. In other words, there is no blueprint for the organism, but rather each cell deploys genetic information and adjusts its status to signals coming from the surrounding cellular environment, as well as from the environment external to the organism itself."

The need to move beyond classical genetics is even more pressing when we turn our attention from development to evolution. At best, neodarwinism is perceived to provide relatively few of the answers needed. The "current frontiers of theoretical evolutionary biology" have moved. Further comments on this are found here and here.

An example from Pigliucci and Boudry follows.

"Eva Jablonka and Marion Lamb have gone in some sense a step further and attempted to formalize a broader view of evolutionary change, which depends on the existence of not one but four mechanisms of inheritance: first, the standard genetic system; second, a panoply of epigenetic heritable effects, based on recently or newly discovered phenomena, such as differential methylation of genes, alterations of chromatin structure, so-called interference RNAs,7 and changes in conformation of proteins (e.g., prions), to mention a few; third, behavioral inheritance, mediated through the ability of some animal species to mimic each other's behavior without having it to be "inscribed" in their genes; and fourth cultural inheritance, which is limited to humans and perhaps a few other species of primates, but which has had an obviously disproportionate effect on the recent history of our planet."

The conclusion of all this is that education and research needs to refocus: away from the molecular revolution which is proving increasingly unproductive.

"The preceding discussion, we argue, shows that the limitations intrinsic in metaphors such as 'genes as blueprints' and the like are not just deleterious for science education - which would be bad enough. They actually misdirect or partially derail thinking about what sort of research programs biologists ought to carry out and how. While there is no question that the "molecular revolution" has been a central and positive development in biology, and indeed in science in general, throughout the second part of the 20th century, it is also becoming increasingly clear that the ultra-reductionist approach inspired and fueled by machine-information metaphors is running out of steam and needs to be replaced with more sophisticated and realistic thinking (a kind of reasonable, or non-greedy reductionism, so to speak). Is it then time to retire metaphors like blueprints and machines, and to seek an alternative way to conceptualize biological organisms, or would it perhaps be better to abandon the use of metaphors in this field altogether?"

Anyone reading the abstract of this paper would think that the "bad science" references relate to ID arguments. However, this is not the focus of their arguments! The authors are actually writing about the failure of the Modern Synthesis to understand both development and the processes of evolutionary transformation. They spend most of their critical discussion on the 'genome as blueprint' metaphor. It may surprise most readers to know that few, if any, ID scholars use the analogy outside the context of protein synthesis within the cell. They do not use this metaphor to suggest that the blueprint comprehends all aspects of reproduction and development. I am familiar with ID scholars questioning genetic-reductionism along the lines followed by Pigliucci and Boudry, and arguing that development needs some information-rich organismally-orientated thinking. Similarly, ID scientists critique the approach of the Modern Synthesis to evolutionary theory in much the same way as Pigliucci and Boudry have done. So there is much common ground here. The main complaint appears to be that ID scientists use metaphors to suggest that natural objects are actually intelligently designed. They are comfortable with the thought that the living world evidences features that bear witness to intelligent agency. They make use of analogies between human designs and natural phenomena because they infer intelligent agency for both categories. However, this has not led to bad science. Allowing that analogies are always partial, there should be no difficulty recognising the immense benefits that have come to science by pursuing this approach. Historical examples are easy to find; some recent examples are here and here and here.

Why Machine-Information Metaphors are Bad for Science and Science Education
Massimo Pigliucci and Maarten Boudry
Science and Education, Online October 2010 | DOI: 10.1007/s11191-010-9267-6

Abstract: Genes are often described by biologists using metaphors derived from computational science: they are thought of as carriers of information, as being the equivalent of "blueprints" for the construction of organisms. Likewise, cells are often characterized as "factories" and organisms themselves become analogous to machines. Accordingly, when the human genome project was initially announced, the promise was that we would soon know how a human being is made, just as we know how to make airplanes and buildings. Importantly, modern proponents of Intelligent Design, the latest version of creationism, have exploited biologists' use of the language of information and blueprints to make their spurious case, based on pseudoscientific concepts such as "irreducible complexity" and on flawed analogies between living cells and mechanical factories. However, the living organism = machine analogy was criticized already by David Hume in his Dialogues Concerning Natural Religion. In line with Hume's criticism, over the past several years a more nuanced and accurate understanding of what genes are and how they operate has emerged, ironically in part from the work of computational scientists who take biology, and in particular developmental biology, more seriously than some biologists seem to do. In this article we connect Hume's original criticism of the living organism = machine analogy with the modern ID movement, and illustrate how the use of misleading and outdated metaphors in science can play into the hands of pseudoscientists. Thus, we argue that dropping the blueprint and similar metaphors will improve both the science of biology and its understanding by the general public.