Is Systems Biology valid science?

No because your claim yesterday was a blanket attack on all evolutionary science, not a single paper on the evolution of eukaryotes. That’s why Dr. Swamidass pointed out there are tens of thousands of papers on the subject which you claimed were ALL a waste and unscientific , your words.

I find your bait-and-switch now to be quite disingenuous. Did you intend to be deceptive that way?

Leave him alone @Timothy_Horton. This was a veery conciliatory note:

Take the win and move one.

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Actually it was a lame attempt at distraction and which had nothing to do with his claim yesterday I was referring to. But if you’re happy allowing such subterfuge, so be it.

Did the Amoeba proteus have mitochondria before it injested the bacteria?

This is factually incorrect and is an argument apparently made from rather severe ignorance of actual evolutionary biology.

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But have you cited any research papers yet, pawas? Do you realize that there are very different types of papers?

I don’t see the point of citing only two papers that don’t contain any new research, then complaining that they are too speculative. You’re also going in the pseudoscientific direction of concentrating on rhetoric and ignoring the data.

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No need to move the goal posts @DaleCutler.

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It was an honest question.

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Sure it was. The answer is “yes”. But why do you care?

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Yes it was. Thank you. Why do you care why I care? :slightly_smiling_face:

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An Introduction to Systems Biology: Design Principles of Biological Circuits
by Uri Alon

Product description

Thorough and accessible, this book presents the design principles of biological systems, and highlights the recurring circuit elements that make up biological networks. It provides a simple mathematical framework which can be used to understand and even design biological circuits. The textavoids specialist terms, focusing instead on several well-studied biological systems that concisely demonstrate key principles.

An Introduction to Systems Biology: Design Principles of Biological Circuits builds a solid foundation for the intuitive understanding of general principles. It encourages the reader to ask why a system is designed in a particular way and then proceeds to answer with simplified models.

Review

“[This text deserves] serious attention from any quantitative scientist or physicist who hopes to learn about modern biology. [It is] well written. … Alon’s book is the better place for physicists to start. It assumes no prior knowledge of or even interest in biology. Yet right from chapter 1, the author succeeds in explaining in an intellectually exciting way what the cell does and what degrees of freedom enable it to function. … The book proceeds with detailed discussions of some of the key network motifs, circuit-element designs … [and] focuses on concrete examples such as chemotaxis and developmental pattern formation. … He draws the detailed strands together into an appealing and inspiring overview of biology. … One final aspect that must be mentioned is the wonderful set of exercises that accompany each chapter. … Alon’s book should become a standard part of the training of graduate students in biological physics… .”
―Nigel Goldenfeld, University of Illinois at Urbana-Champaign, Physics Today , June 2007

“…a superb, beautifully written and organized work that takes an engineering approach to systems biology. Alon provides nicely written appendices to explain the basic mathematical and biological concepts clearly and succinctly without interfering with the main text. He starts with a mathematical description of transcriptional activation and then describes some basic transcription-network motifs (patterns) that can be combined to form larger networks. … Alon investigates networks at a higher level, including genomic regulatory networks. He does an excellent job of explaining and motivating a useful toolbox of engineering models and methods using network-based controls. … will be a valuable and non-overlapping addition to a systems-biology curriculum.”
―Eric Werner, Department of Physiology, Anatomy and Genetics, University of Oxford, Nature, Vol. 446, No. 29, March 2007

“I read Uri Alon’s elegant book almost without stopping for breath. He perceives and explains so many simple regularities, so clearly, that the novice reading this book can move on immediately to research literature, armed with a grasp of the many connections between diverse phenomena.”
―Philip Nelson, Professor of Physics, University of Pennsylvania, Philadelphia, USA

“… Beyond simply recounting recent results, Alon boldly articulates the basic principles underlying biological circuitry at different levels and shows how powerful they can be in understanding the complexity of living cells. For anyone who wants to understand how a living cell works, but thought they never would, this book is essential.”
―Michael B. Elowitz, California Institute of Technology, Pasadena, USA

“Uri Alon offers a highly original perspective on systems biology, emphasizing the function of certain simple networks that appear as ubiquitous building blocks of living matter. The quest for simplicity ― without losing contact with complex reality ― is the only way to uncover the principles organizing biological systems. Alon writes with uncommon lucidity…”
―Boris Shraiman, University of California, Santa Barbara, USA

“This is a remarkable book that introduces not only a field but a way of thinking. Uri Alon describes in an elegant, simple way how principles such as stability, robustness and optimal design can be used to analyze and understand the evolution and behavior of living organisms. Alon’s clear intuitive language and helpful examples offer ― even to a mathematically naive reader ― deep mathematical insights into biology. The community has been waiting for this book; it was worth the wait.”
―Galit Lahav, Harvard Medical School, Boston, Massachusetts, USA

+++++++

Dave Morris
One of the best textbooks I’ve ever read
December 27, 2013
“There were several times during my first reading of this book when my jaw literally dropped at how cool biological systems are.”

Just “cool”? :slight_smile:

+++++++

young250
New Topic Well Written.
October 21, 2016

“Got this as textbook to a course that discuss what we can learn from biological systems and apply the concepts into circuit and control system designs. Really interesting topic and well written book. Things are explained in really simple language and easy to comprehend”

+++++++

Robust Design of Biological Circuits: Evolutionary Systems Biology Approach

Journal of Biomedicine and Biotechnology
Volume 2011, Article ID 304236, 14 pages
DOI: 10.1155/2011/304236
Research Article
Bor-Sen Chen, Chih-Yuan Hsu and Jing-Jia Liou

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pawas, no one wants to hear this. Darwinism is dead.

4 posts were split to a new topic: Comments on Systems Biology

Systems Medicine—Complexity Within, Simplicity Without

Richard Berlin, Russell Gruen, and James Best
J Healthc Inform Res. 2017; 1(1): 119–137.
PMCID: PMC5491616
DOI: [10.1007/s41666-017-0002-9]
PMID: [28713872]

Additional biologic explanation is required when the reductionist approach is inadequate, when components are missing or cannot be described satisfactorily. Systems Theory is one such additional framework, a focus on the whole early in discovery to determine overlying principles that then guide the individual components (considered top down) rather than the reductionist bottom up approach to understanding.

Systems Biology is a comprehensive, quantitative, and dynamic study of organisms.

The Human Physiome Project (HPP) is a global network of research centers working on physiology and organ system function, from molecule to cell to organ and body taking inspiration from Systems Biology.

Questions remain on how to merge this immense amount of data and how to construct consistent grand models involving dispersed datasets. It is not certain that the application of big data solutions alone can actually address these concerns

Another area in physiology which advances with the aid of Systems Biology is the study of -omics (genomics, transcriptomics, proteomics, metabolomics).

The data sets generated and the pathways described, now so many and cascading, require overarching views to simplify and bring further understanding to human biology. The search for organization continues. Not that the work on the genome or -omics or biomarkers is any less important; rather, one recognizes that crucial structure is still missing, an organizing hierarchical order. Complexity begets complexity without organization. A system of systems containing functions and processes requires principles regarding how they relate and interact. This is important for understanding, for communication, and to produce coherence as subunits and subsystems are assembled to represent a total organism. Organizing principles are needed

Medicine is at a major transition point in history. Systems Theory offers organizing principles, holism, and a framework for emergent properties to form the basis for Systems Medicine. Maintaining complexity within at the leading edge of science, Systems Medicine must provide simplicity without for the human.

What do you mean by “dead”?

According to NIH’s Eugene Koonin*, it just takes time:

a coherent understanding of “how it works” is slowly but steadily emerging in evolutionary biology. However, one has to face the facts: first, it is a slow process, and we are still far from the goal; second, the emerging picture is highly complex and, furthermore, makes little sense without mathematical theory. Thus, communicating modern evolutionary biology (as opposed to deceptively simple antiquated ideas) is indeed a daunting task.

The very approach to evolutionary studies has changed completely. Not only the fact of evolution itself but the existence of deep evolutionary connections between different domains of life — to be concrete — evolutionary connections between, let us say, mammals, such as humans, and prokaryotes, bacteria and archaea, have become indisputable. These findings make questioning not only the reality of evolution but the evolutionary unity of all life on earth completely ridiculous and outside of the field of rational discourse.

Lynch wrote in one of his papers: “Nothing in evolution makes sense except in the sense of population genetics.”

Population genetics is a mathematical framework that is essential for building evolutionary theory but it is not the theory itself. The Modern Synthesis does employ that framework and is a correct theory but only for a narrow range of evolutionary processes in certain groups of organisms. It is quite a typical situation in science, actually.

genomes are dynamic systems evolving in space and time not static collections of genes. But it is also OK to view them as entities, information storage devices. These viewpoints are complementary.

any actively working scientist in evolutionary biology probably realizes that the Modern Synthesis or neo-Darwinism, or whatever the name is, is insufficient in the post-genomic era. This is a set of concepts that is insufficient for understanding the entirety of evolution. It doesn’t mean it’s wrong. It’s only becoming wrong if someone claims that they need nothing past the concepts in the Modern Synthesis.

if biology is to evolve into a “hard” science with a solid theoretical core, it must be based on null models, no other path is known.

In any field, null model is the simplest explanation of the available data that does not violate physical laws. Good and sensible scientific practice in physics but also in other sciences. Scientists first come up with the simplest rational explanation of the available data and then see if anything in the data refutes that explanation and requires a more complex model. And so on and so forth.

(*) Eugene Koonin: “The New Evolutionary Biology”. Suzan Mazur. HuffPost. Updated Feb 04, 2018

Life is Physics: Evolution as a Collective Phenomenon Far From Equilibrium
Nigel Goldenfeld and Carl Woese
DOI: 10.1146/annurev-conmatphys-062910-140509

condensed matter physics concepts might provide a useful perspective in evolutionary biology, the conceptual failings of the modern evolutionary synthesis, the open-ended growth of complexity, and the quintessentially self-referential nature of evolutionary dynamics.

[emphasis added]

Perhaps I’m not qualified to criticize Dr. Koonin’s statements, because my biology education is slightly weaker than his. :slight_smile:
BTW, it seems evident that the famous NIH scientist isn’t philosophically close to ID Sealions. However, sometimes appearances could be deceiving. :slight_smile:

Let’s be patient. In the meantime, let’s try our best to understand biology better. This may require much reading and studying. Some of us -lacking strong biology education- may have to ask more questions in order to get it. But there are nice folks willing to politely answer technical questions, no matter how dumb those questions might sound. See an example under another topic. That conversation is still ongoing. It’s very slow because there’s a drastic difference in biology education level between the conversants. But note that all the questions raised so far have been clearly answered with sufficient details.

Let’s use -as illustration- a history analogy, like the “Napoleon in Russia” that you liked so much. :slight_smile:

However, not a story from Eastern Europe but from China. Specifically about a famous person in that country.

In China perhaps you may criticize the Darwinian idea, but, at least according to somebody who apparently knows quite a bit about that country:

Mao is still an important figure in the Party though he has been dead for decades. And most of Chinese still have to learn about his deeds and ideology in schools no matter if you like it.

you can hardly publicly say Mao should retire because it is politically incorrect and will be condemned by the domestic media.

Text quoted from here:

https://www.quora.com/Should-Mao-Zedongs-portrait-be-retired-and-removed-from-Tiananmen

Don’t expect that the textbooks apparently implying that “the Galapagos finch beak adaptation mechanisms can be easily extrapolated to the whole ToL” will be rewritten anytime soon.

PS. My wife and I toured a few cities in that country a decade ago and took pictures with that portrait in the background. Sorry, but -as far as I recall- Napoleon wasn’t seen anywhere there. :slight_smile:

@pawas, we have covered this in depth elsewhere. Darwinism as commonly understood is not the whole story of evolutionary science: The Neutral Theory of Evolution.

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Then why don’t you make an argument that the prokaryotic to eukaryotic transition is well understood? Your assertions based on your own ignorance are not very interesting.

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Excellent! Thanks for the information.

Can we move posts #186 and #187 out of here to that sideline topic? Actually, can we move all the off-topic posts to that sideline topic? That would include my own replies that are off-topic too. That would make this topic less cluttered. Thanks.

Mung,

Check this out:

You may want to look into that topic for more information on the state of affairs in the evolution discussion. I’m not a big fan of discussing that topic for too long. It’s not exactly WYSIWYG type of deal. Engineers are generally a little picky about topics. We like to understand exactly how currently observed things function, interconnect and communicate.

I like to understand the biological circuits with feedback and feed forward loops and robustness and optimization issues and the whole nine yards. That’s the kind of “goodies” Systems Biology provides that evolutionary discussions don’t. The evo-devo topic may have a little flavor, because it doesn’t have much “evo”. It’s mainly “devo” stuff.

This current topic is about Systems Biology and now Systems Medicine too, as you saw a few posts ago. Everything else is off-topic.

Thanks for your understanding.

:slight_smile:

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