Does Systems Biology reveal anything that traditional biology wouldn’t?
Why are non-biology professionals (computer scientists, control system engineers, mathematicians, physicists) getting involved in interdisciplinary biology research teams lately? Are they really needed? Why?
Are there biologists who consider that Systems Biology is not serious biology?
Is there a question or a point your are offering here?
Are any of the systems in the cell a mechanical system?
That’s a very interesting question. I think biology deals with many physical processes that may qualify as mechanical. Have you seen any recent reference to this written somewhere?
By the way, Uri Alon is also the author of An Introduction to Systems Biology: Design Principles of Biological Circuits
Here’s an example of “Systems Biology” issues. Note the language used seems related to engineering stuff. It’s really interesting, isn’t it? For those of us coming from the systems engineering background, this is fascinating.
Despite employing diverse molecular mechanisms, many different cell signaling systems avoid losing information by transmitting it in a linear manner.
the cells building a multicellular organism sense chemical gradients to determine their position and send and receive chemical signals to communicate.
signaling is far more complex, with different pathways operating via different molecular components and biochemical mechanisms.
such complex signaling mechanisms can carry out sophisticated signal processing.
wonder why so many quantitative biologists neglected to study linear input-output signaling for so long
the consequences of this linearity included maximal information transmission and an increased robustness of the output to random downstream molecular events
One challenge in biology is to make sense of the complexity of biological networks.
We find an unexpected convergence: the three pathways behave in some physiological contexts as linear signal transmitters.
linearity arises through different means in each pathway
Linearity is a desired property in engineering where it facilitates fidelity and superposition in signal transmission. Our findings illustrate how cells tune different complex networks to converge on the same behavior.
Cells must continually sense, interpret, and respond to their environment. This is orchestrated by signaling pathways: networks of multiple proteins that transmit signals and initiate cellular response
the canonical Wnt pathway, the ERK pathway, and the Tgfβ pathway have converged upon a shared strategy of linear signal transmission.
despite their distinct architectures, the three signaling pathways behave in some physiological contexts as linear transmitters.
complexity of each pathway might afford tunability, in the sense that parameters can be tuned to produce different behaviors in different contexts.
many biochemical processes are inherently nonlinear, meaning that linearity does not arise from a reduction in complexity.
linearity emerges from complex interactions
analogous to engineered systems, complexity in the biochemical pathways we analyzed here might have evolved in part to produce linearity.
I would say yes, in the same way that there are mechanical systems in geology and cosmology.
Modern philosophy of science has distanced itself from the historical usage of ‘mechanical’, and in particular “from both the idea that mechanisms are machines and especially from the austere metaphysical world picture in which all real change involves only one or a limited set of fundamental activities or forces”
Instead, mechanism is defined more generally, such as
With this in mind, do you think mechanism is a helpful explanatory framework for some or all of the processes of a living cell? Could a cell be thought of as a hierarchy of mechanisms?
Quotes are from the SEP article on mechanisms
https://plato.stanford.edu/entries/science-mechanisms/
The “orchestrated” part would be the only sticking point. Cells and their cellular pathways are deterministic in many ways. “Orchestrated” carries a lot of philosophical baggage, especially in conversations like the one in this thread.
Fair enough. That word needs unpacking which I’ll defer to the SEP article and its citations. There are other definitions which of mechanism there which avoid that word.
The philosophical usages of orchestration are definitely not meant to invoke design in the sense that it requires a designer or teleology as in Aristotle’s sense of final cause (Hi Mung!).
It is good to see an engineer who is fascinated by biology. At PS, one often sees engineers who push intelligent design because they think their engineering training gives them more insight into biology than biologists.
Seems to me that even orchestration is mechanical. 
I suspect you are making a pun on “systems” biology with this reference to how that the term is used in computer systems.
But in one way, you are on the right track: to understand how a term is used as a term of art in the theory in some field, you have to understand the theory it is part of. But here the theory is philosophy, and in particular the theory in the paper that proposes this definition involving ‘orchestration’.
If this reminds you of discussions of the meaning of ‘fitness’ in biology, right you are.
Can somebody elaborate on the following statement?
The authors likely would have said that it might have evolved to produce linearity, or it might evolved for some other reason, but it surely evolved.
As the question of the OP, yes systems biology is valid science, or at least it can be valid science. It is, however, becoming somewhat of a grab bag of different fields, and is trending downwards as a term. It is new enough and broad enough of a feel that it lacks a sharp definition.
Can you point to the literature that explains how that could have happened? Not how it happened, but just how it could have happened, based on the laws of physics and chemistry?
There are literally 10s of thousands of papers and studies developing how this could have evolved. It is hard to know where to begin.
According to what is written in many research papers, speculation in this area is quite abundant, and I have a personal preference for disliking that.
The coherent and comprehensive explanation of the appearance of Eukaryota must be so solidly founded that it should be available in textbooks and video courses. For example, MIT offers many free online courses, like the developmental biology online course by Professor Hazel Sive. Developmental Biology is fully WYSIWYG stuff. Very little speculation, if any at all. Evolutionary biology does contain a substantial speculative component, specially in the macro-evolution area. The evo-devo area has much more devo than evo.
How much of the scientific literature on the topic have you actually read? Can you list a few published papers and explain why they are not scientific?
@Timothy_Horton has a point…
I somehow doubt you have read many of the 10s of thousands of papers. Would be willing to share your reading list?