Hi Gregory,
“You write: "molecular biology is permeated with engineering concepts"
On what basis do you claim this, i.e. that concepts have been 'transferred' from engineering to molecular biology? “
For starters, simply go back to my original posting.
First, take the manner in which a mainstream, non-controversial molecular biologist would describe the process of protein synthesis:
To make a protein, a molecular machine, known as the ribosome, translates a messenger RNA molecule using the genetic code.
Now step back and ponder where the terms machine, message, translate, and code came from.
Second, consider the quote from Lewontin:
“Many biologists in the late 1950s (I among them) regarded with a certain contemptuous hauteur the attempts of renegade physicists to illumine the relation between gene and protein by engaging in the sort of cryptanalysis that became so romantic as a result of the wartime triumphs of Bletchley Park. But Kay shows quite convincingly that, although these codebreaking techniques could not in themselves provide the right answer, *the view of DNA as code and amino acid sequence as plaintext was absolutely essential in the very conception of the critical experiments at the beginning of the 1960s.* The brilliant paper by Crick, Barnett, Brenner, and Watts-Tobin, which demonstrated so elegantly that the DNA sequence was processed from a fixed starting point using each successive non-overlapping triplet to determine the next amino acid in the chain, and Nirenberg and Matthaei's path-breaking demonstration that poly-U RNA in an in vitro synthetic system resulted in the construction of a polypeptide consisting solely of phenylalanine, *would have been conceptually impossible without the metaphor of the code.* “
Lewonton is, of course, reviewing Lily Kay’s book, Who Wrote the Book of Life. This is a fascinating read that carefully documents how various concepts have been transferred from engineering to molecular biology.
Gregory: “Second, are you suggesting that molecules are themselves 'machines' (i.e. cellular mechanisms) or that saying they are 'like machines' is an effective way to speak about them?”
Water is a molecule and it is not a machine. But in molecular biology, the term ‘machine’ has become very popular when describing protein complexes – molecular machines. In his 1998 essay (note the title – “The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists”), Alberts explains:
“Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like the machines invented by humans to deal effi ciently with the macroscopic world, these protein assemblies contain highly coordinated moving parts.”
I think we can go further than this, but let me simply answer your question – I think of protein machines as machines rather than merely being like machines.
Gregory: “To me, organisms and machines are simply not the same thing, they are not equivalent and shouldn't be confused (the scene in Kubrick-Spielberg's AI where the human-boys are circling the 'robot-boy' near the pool chanting ORGA-MECHA gets most keenly at this issue).”
I would agree that organisms and machines are not the same thing. But a molecular machine is not an organism.
“Yet if biologists find engineering concepts attractive on the basis that it helps them to understand the structures, systems and information they are observing in nature, then why not incorporate or collaborate or even let the engineers loose on human nature?”
Give it time. Neuroscience has been making great strides and it is yet another area in biology heavily indebted to molecular biology.
“It almost appears that you are advocating biologists to re-define concepts from 'outside' discplines into their own. Or we could call it sharing.”
I’m not advocating here, merely observing what has happened and is happening.
“In this case, it is importing 'mechanistic' language into a natural scientific field. Do you worry about this in any way?”
Such language and concepts continue to be imported because they turn out to be so fruitful. No, I don’t really worry about it, but perhaps this is because I have not thought through all the implications. Is there is a reason I should be worried?
“The simplest question in this message for the last: Aren't machines also 'constructed' and 'made,' in addition to being 'designed'?”
Indeed.
- Mike
Hi Mike,
I've been pondering over your recent thoughts here for sometime on this topic, but probably only have some basic questions to ask you, and that as an outsider both to molecular biology and engineering.
You write: "molecular biology is permeated with engineering concepts"
On what basis do you claim this, i.e. that concepts have been 'transferred' from engineering to molecular biology? Are you suggesting that biologists are reading engineering journals and realising that certain concepts may also express linguistically what they are observing in their biological laboratories and in the field? Or perhaps are there engineers who have sought a new profession in molecular biology and thus 'imported' their ways of thinking from engineering into the new field? (The latter example of interdisciplinarity may be rare from engineering to biology, but it holds more easily in other areas of study.) Or perhaps there is some other explanation you have for how the ideas and language are spreading from one respective field to another?
Second, are you suggesting that molecules are themselves 'machines' (i.e. cellular mechanisms) or that saying they are 'like machines' is an effective way to speak about them? To me, organisms and machines are simply not the same thing, they are not equivalent and shouldn't be confused (the scene in Kubrick-Spielberg's AI where the human-boys are circling the 'robot-boy' near the pool chanting ORGA-MECHA gets most keenly at this issue). Yet if biologists find engineering concepts attractive on the basis that it helps them to understand the structures, systems and information they are observing in nature, then why not incorporate or collaborate or even let the engineers loose on human nature?
It almost appears that you are advocating biologists to re-define concepts from 'outside' discplines into their own. Or we could call it sharing. In this case, it is importing 'mechanistic' language into a natural scientific field. Do you worry about this in any way?
The simplest question in this message for the last: Aren't machines also 'constructed' and 'made,' in addition to being 'designed'?
Cheers,
Gregory
p.s. the cells are computers analogy or parallel, as you say earlier, would seem to lead down the road to Kurzweil's suggestion that we are 'Spiritual Machines.'
Over at Telic Thoughts, there is a new contributor who uses the handle Techne. Techne has posted a nice review of a new paper by Antoine Danchin from the Pasteur Institut entitled, “Bacteria as computers making computers.”
http://telicthoughts.com/happy-new-year-computers-making-computers/
While I have yet to read the paper, it appears Danchin’s paper further supports my contention that molecular biology is permeated with engineering concepts. Techne quotes the following excerpt:
“Historically, systems biology follows on from molecular biology, a science based on many concepts more closely linked to arithmetic and computation than to classical physics or chemistry. Molecular biology relies heavily on concepts such as ‘control’, ‘coding’ or ‘information’, which are at the heart of arithmetic and computation. To accept the cell as a computer conjecture first requires an exploration of the concept of information, in relation to the concept of genetic program.”
After raising many interesting points, Techne concludes:
“The article continues to discuss at length the parallels between our own created information processing systems (computers) and molecular processes fundamental to life. With more and more information being gathered on cellular mechanisms, cells can be seen as computers (machines expressing various programs), that are not only able to govern cellular processes needed to sustain the software, but also contains the necessary software and machinery to reproduce the computing machine while replicating its program. The article is sure to provide information for many more interesting blog discussions.”
- Mike
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Received on Thu Jan 1 18:07:25 2009
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