Why Naturalists, Materialists and Atheists Are Scared of 'Design in Nature' and 'Machine Metaphor'

The Muslim scholar Ibn al-Qayyim (d. 1350) said: "Whoever reflects upon the whole universe, its upper and lower [parts] and all of its domains will find it bearing witness to the affirmation of its maker, originator and owner." Madārij al-Sālikīn (1/82)

According to Wikipedia, Massimo Pigliucci is a "Professor of Philosophy at CUNY-City College, formerly co-host of the Rationally Speaking Podcast, and formerly the editor in chief for the online magazine Scientia Salon. He is an outspoken critic of pseudoscience and creationism, and an advocate for secularism, science education."

Pigliucci wrote a paper in 2010 with Maarten Boudry (another philosopher and skeptic) titled: "Why Machine-Information Metaphors are Bad for Science and Science Education", and it was published in the Science and Education Journal.

In summary, what they are saying is that the use of metaphors that involve machines, computers, codes, information transfer, factories and so on for biological organisms and life should be dropped because they allow "creationists", "intelligent-designers" and so on to make their "spurious case".

Some quotes the paper:

Scientific thinking and education are rife with the use of metaphors... In biology and biological education in particular, metaphors are pervasive at almost every level of description and explanation. Brown (2003, p. 159) has even argued that "biology today reveals more forcefully than any other area of science the essential role of metaphor in scientific reasoning and communication." Perhaps this pervasiveness of metaphors is an inevitable result of the way human beings think (Lakoff and Johnson 1980; De Cruz and De Smedt 2010), but it has consequences for both science education and scientific research, and not necessarily for the better.

In response to the above, the reason why these metaphors are pervasive is because, as we have explained elsewhere:

Innate human faculties unavoidably generate beliefs of design, order and purpose which are rationally legitimate and warranted. Marks of design and purpose are recognized perceptually and implicitly (innately) and from here the inferential step to a designer is natural, minimal, rational and warranted. Such marks include contrivance, order, organization, intent, purpose, law-like behaviour, pursuit of goals or outcomes or goal-steering mechanisms, regularity, beauty and adaptation. This itself is the very source of the rational justification for science and the scientific method, since the scientific method has underlying assumptions that cannot be verified by the scientific method itself, and must be assumed. It is therefore not possible to separate innate beliefs about the universe from scientific inquiry and the scientific enterprise as a whole. This is why up until the 19th century, and in the entire history of humanity--with very rare exceptions--all scientific research was conducted by believers in a Creator on the basis that they were studying the mechanisms in creation--the ways and means, the causes and effects, the handiwork of the Creator--in order to gain further enlightenment about the Creator. Likewise, to exploit their findings to facilitate human progress. The entire scientific enterprise rests upon the assumptions that the universe is real, material, orderly, designed, consistent and rationally investigable. This is why it is impossible to erase the innate disposition (fiṭrah)--in which belief in a Creator is permanently embedded--through any amount of materialist brainwashing within the lifecycle of education. It is why people will always be inclined towards belief in God and the desire to worship a Creator." (This is Islam, 1st edition, 2018, p.8).