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Uncommon Descent Contest Question 6: Why waste a crisis, especially in genomics?


Here’s On the Epistemological Crisis in Genomics by Edward R Dougherty, which moved in Current Genomics, April 2008.


There is an epistemological crisis in genomics. At issue is what constitutes scientific knowledge in genomic science, or systems biology in general. Does this crisis require a new perspective on knowledge heretofore absent from science or is it merely a matter of interpreting new scientific developments in an existing epistemological framework? This paper discusses the manner in which the experimental method, as developed and understood over recent centuries, leads naturally to a scientific epistemology grounded in an experimental-mathematical duality. It places genomics into this epistemological framework and examines the current situation in genomics. Meaning and the constitution of scientific knowledge are key concerns for genomics, and the nature of the epistemological crisis in genomics depends on how these are understood.

He kvetched,

The rules of the scientific game are not being followed. Given the historical empirical emphasis of biology and the large number of ingenious experiments that have moved the field, one might suspect that the major epistemological problems would lie with mathematics, but this is not the case. While there certainly needs to be more care paid to mathematical modeling, the major problem lies on the experimental side of the mathematical-experimental scientific duality. High-throughput technologies such as gene-expression microarrays have lead to the accumulation of massive amounts of data, orders of magnitude in excess to what has heretofore been conceivable. But the accumulation of data does not constitute science, nor does the a postiori rational analysis of data.

What’s happened since? Another black hole?

Okay, so the sixth Contest question, for a free copy of Expelled?, is: What rules of science are relevant for genomics? Are they being followed? Remember, 400 words or less, and I recommend that you read the article first.

Contest rules, in general, are here, but most are pretty obvious.

I don't participate here much. I pop in now and then and for the most part just read. But I am amazed that there is not more interest in this topic... Since I consider all three of these posts to be relevant, and together they are over 400 words, I will excuse myself from any prize. I already have the DVD anyway. This whole philosophical mess of a paper by professor Dougherty is astonishing! I simply must vent. I will answer my own question... I asked, 'who is Dougherty'? Look no further than his paper. He is Emmanuel Kant and David Hume. He is also Fredrick Nietzche and Roland Barthes (there are more). After paying lip service to the laws of logic and invoking a keen observation of Einstein, Dougherty talks about mathematics (not common language) as being the supreme rule for elucidating reality scientifically. If that is so, why does he attempt to reason with us, using common language? Mr. Dougherty, would you care to express that proposition mathematically? His paper is not a scientific paper. It is a circular philosophical journey lamenting the non-existence of an epistemology to intuit the genome. Unless I have totally misunderstood him, he seeks meaning by which to understand genomics, yet insists on rules (mathematical language) that cannot provide it. This assault on common language is not new. Consider Roland Barthes in his essay, The Death of the Author: “Refusing to assign a secret, ultimate meaning to a text liberates what may be called an anti-theological activity; an activity that is truly revolutionary since to refuse meaning is, in the end, to refuse God and his hypostases—reason, science, law.” Now when you couple that with Nietzche's remark, "I'm afraid we are not rid of God because we still have faith in grammar", a familliar pattern emerges. And it started in the garden when Satan suggested to Eve, 'Did God really say?' If we want to make mathematics the only law, then we smuggle in a metaphysic. Nature will always be absurd to materialists because nature (and in particular- life) cannot be described apart from ordinary language. And that is why we are deluged with convoluted philosophical papers about science using ordinary words and not equations. The real test is in the coherence of those ordinary words. And like those who preceded him, Mr. Dougherty must use words to place doubt in our minds about words. There is nothing less mathematical (logical) than that. No Mr. Dougherty. No Mr. Nietzche, Hume, Barthes, and the likes of you. You've got it wrong... 'In the beginning was the Word'. If I have to take someone at their word, among other tests, it will be someone who does not deny the authority of his own words. "...and that's all I have to say about that". (Forrest Gump) Lock
Well no one else seems to be chiming in, so I might add a bit more... In his article, Dougherty (after chiding Dembski along Kantian lines)offers us this queer little spell: "[re: genomics]...The reasons for lacking understanding are different from those in physics, but they are compelling in their own way. Nature is absurd from the human perspective because we lack the categories of understanding with which to intuit it – be it physics or biology." Well there we have it. How typical! A design paradigm can intuit it (and better so than naturalism) but since it isn't naturalism, it isn't scientific. So does that mean that the 'right science'... is the 'right philosphy'? Isn't it reason that founds philsophy? And evidence is secondary and useful to establish the chain of reason? And isn't Dembski the one Doughrety derides for wanting more of a return reason? Seems to me that C.S. Lewis talked about the simplicity of this problem in his book Miracles. He said (paraphrasing) that men could study the patterns in the dots of a painting and discover all kinds of real and relevant laws. But the patterns are only an after effect. The painting was never about the many arbitrary rules found in studying the dots. Lewis, as usual, made his point well. Yet, simple as it may be, these boys are insidious. They start out from the stance that we cannot know (it's absurd, Kant, etc...), and then restrict the use of reason to observe only dots in a larger fabric. God forbid we use that same reason to look at the picture as a whole with what dots we have as yet. Correction... God doesn't forbid it, Emanuel Kant does. I guess (one way or another), there is an Emanuel who lives to this day. He is claiming by decree to be God. And he has many worshippers. Personally, if the establishment of scientists wants to claim they don't know, and that genomics is absurd, I can accept that. I already knew they were lost. I am only grateful I no longer have to worship their high priests. Myself and many others have God first to thank, but also the likes of Dembski, Johnson, and Behe et al. Which reminds me, who is Dougherty? Lock
From Edward R Dougherty: "But the accumulation of data does not constitute science, nor does the a postiori rational analysis of data." I assume he uses an a priori framework with which to make that judgement? Of course he does. And rightly so. And that lens is the one science should be using (and does... but not consistently). Here is the insanity... science uses this lens religiously, except that when doing so the evidence points to religious conclusions. Denyse, you asked: "What rules of science are relevant for genomics?" Available empirical data examined consistently through the lens of the 'law of non-contradiction'. "Are they being followed?" Really now... is that question necessary? Lock

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