Criticality in Biochemical Networks

J Royal Society Interface

Researchers from our center, in collaboration with State University of New York, Binghamton University and the Instituto Gulbenkian de Ciência developed a mathematical and computational framework to understand how biochemical networks contribute to the evolvability, robustness, and resilience of biological organisms.

In a paper in the journal Journal of the Royal Society InterfaceLuis Rocha, George J. Klir Professor of Systems Science, and Drs. Manuel Marques-Pita and Santosh Manicka (who earned his Ph.D. in complex networks and systems from the Luddy School), show that a large amount of redundancy exists in how genes, proteins and other biochemical components process signals. This results in much robustness to perturbations, allowing biological systems to exist in a stable or near-critical dynamical regime, despite being composed of thousands of biochemical variables which would ordinarily result in chaotic dynamics.

The measure of effective connectivity developed by Rocha and Marques-Pita captures redundancy in automata networks and is shown in the paper to be highly predictive of dynamical regime of biochemical systems ranging from flower development to breast cancer in humans. The approach thus adds empirical validity to several  well-known hypotheses in theoretical biology: 1) that canalization adds robustness to biological development put forth by C.H. Waddington, 2) that redundancy is essential for evolvability put forth by Michael Conrad, and 3) that biological organisms exist in a near-critical dynamical regime put forth by Stuart Kauffman. The new work further connects the three hypotheses by equating canalization with redundancy, providing a  measure of effective connectivity based on dynamical redundancy, and further showing that this measure very accurately predicts the dynamical regime of biochemical networks.

You can read the article following the links in reference:

Manicka Santosh, Marques-Pita Manuel and Rocha Luis M. [2022]. “Effective connectivity determines the critical dynamics of biochemical continue reading.

CSBC researchers show rise and fall of rationality in language (PNAS)

This new paper is the result of a long-standing collaboration between CSBC director Johan Bollen and Marten Scheffer, Ingrid van de Leemput, and Els Weinans of Wageningen University: “The rise and fall of rationality in language”

Summary:

“The post-truth era has taken many by surprise. Here, we use massive language analysis to demonstrate that the rise of fact-free argumentation may perhaps be understood as part of a deeper change. After the year 1850, the use of sentiment-laden words in Google Books declined systematically, while the use of words associated with fact-based argumentation rose steadily. This pattern reversed in the 1980s, and this change accelerated around 2007, when across languages, the frequency of fact-related words dropped while emotion-laden language surged, a trend paralleled by a shift from collectivistic to individualistic language.”

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CSBC researchers discover surge in cognitive distortions since the 1980s

In a study published in PNAS, “Historical language records reveal a surge of cognitive distortions in recent decades,” CSBC researchers in the Luddy School of Informatics, Computing, and Engineering and colleagues at IU’s Department of Psychological and Brain Sciences analyzed millions of books published over the past 125 years. They discovered that, since the 1980s there has been a surge of language indicative of “cognitive distortions,” thinking patterns usually seen in internalizing orders such a depression and anxiety.

The paper results from a interdisciplinary collaboration between CSBC members Johan Bollen, Alexander Barron, Marijn ten Thij, Psychology and Brain Sciences faculty Lorenzo Lorenzo-Luaces and Lauren Rutter, Provost Professor of Germanic Studies Fritz Breithaupt, and Marten Scheffer of Wageningen University.

“Our analysis of the language used in a collection of more than 14 million books published from 1855 to 2019 in the United States, and German-, and Spanish-speaking countries, reveals a worrisome pattern,” Bollen said. “We see a pronounced ‘hockey stick’ pattern in which the use of cognitive distortion expressions surged well above historical levels in recent decades, including those of the great depression, and World War I and II, after declining or stable levels for most of the 20th century.”

The full press release can be found here

Full paper details:

Historical language records reveal a surge of cognitive distortions in recent decades Johan BollenMarijn ten ThijFritz BreithauptAlexander T. J. BarronLauren A. RutterLorenzo Lorenzo-LuacesMarten Scheffer
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Postdoctoral Positions at CASCI

The Complex Adaptive Systems and Computational Intelligence (CASCI) lab at the Systems Science and Industrial Engineering Department, Binghamton University (State University of New York)  is accepting applications for one or more full-time non-tenure track postdoctoral fellows to conduct interdisciplinary research in Complex Networks and Systems applied to various social, ecological, biological, medicine and health problems.

Recent projects at the lab, funded by NIH, NSF, and FCT, Include:

The appointments are full-time for 12 months, with potential to be extended an additional year subject to funding and satisfactory performance. We offer a competitive salary with generous benefits.

The postdocs will be supervised by Prof. Luis M Rocha and join a dynamic and interdisciplinary team embedded in the cross-university Center for Social and Biomedical Complexity (CSBC) and the Center for Collective Dynamics of Complex Systems (CoCo)  that includes systems scientists, biologists, computer scientists, and social scientists. Please contact him for further information.

Basic Qualifications: A PhD is required in Complex Systems, Network Science, Computer or Computational Science, Computational Biology, Applied Mathematics, Physics, Statistics, Artificial Intelligence or related field; a strong background in analysis and modeling of complex systems and networks; and solid programming skills necessary to handle big data and develop large scale simulations. ABD (all but dissertation) candidates may apply but will need the Ph.D. prior to start.

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Congratulations to new PhD Kelly McClinton!

 

Congratulations to CASCI member Kelly McClinton for successfully defending her dissertation entitled “Computationally Modeling Roman Domestic Art and Architecture” on April 23rd 2021. Kelly was co-supervised by Luis Rocha and Bernard Frischer. She completed her PhD degree as a fellow of the NSF-NRT Interdisciplinary training in Complex networks and Systems. Dr. McClinton’s research investigates how computational models, including 3D reconstructions, mixed-media models, complex systems, and machine learning, present unique technological affordances in studying the fragmented material record of ancient Rome, focusing on domestic Roman art and architecture. In addition to Complex Networks and Systems, her dissertation contributes to the fields of virtual heritage, archaeology, and art history. Kelly is now the Assistant Director of the Virtual World Heritage Lab, and this fall, Kelly will be studying at the University of Oxford, and working on a project entitled “Elite Identity in Domestic Space in Rome. Architectural Change and Redecoration in Late Antique Houses” under the supervision of Professor Ine Jacobs… continue reading.

Uncovering the “master switches” of biochemical networks can explain the effects of drugs in the destruction of cancer cells

Researchers from our lab, in collaboration with the Luddy School of Informatics, Computing, and Engineering, the Instituto Gulbenkian de Ciência, and Northeastern University have developed a mathematical framework that increases our ability to explain and control biochemical systems, including those involved in disease.

In a paper featured on the cover of the journal Proceedings of the National Academy of Sciences (PNAS), Professor of Informatics Luis Rocha and Alexander Gates (who earned his Ph.D. in complex networks and systems from the Luddy School), introduce an effective graph that can capture nonlinear logical redundancy present in biochemical network regulation, signaling, and control.

Rion Correia (a member of the CSBC lab, who also earned his Ph.D. in complex networks and systems from the Luddy School and Xuan Wang, a current Ph.D. candidate, and member of the lab) are also working on the project. Together, the authors demonstrate the utility of the approach with computational models of human cancer cells, showing that the effective graph reveals why some cancer medications are more effective than others in killing breast cancer cells.

You can read the full details via the press releases below:

Luddy Press Release

Instituto Gulbenkian de Ciência Press Release

You can read the article here:

https://www.pnas.org/content/118/12/e2022598118

*Those interested in contacting the authors should do so directly, via the links provided above.… continue reading.