Scaling laws in enzyme function reveal a new kind of biochemical universality.

All life on Earth is unified by its use of a shared set of component chemical compounds and reactions, providing a detailed model for universal biochemistry. However, this notion of universality is specific to known biochemistry and does not allow quantitative predictions about examples not yet observed. Here, we introduce a more generalizable concept of biochemical universality that is more akin to the kind of universality found in physics. Using annotated genomic datasets including an ensemble of 11,955 metagenomes, 1,282 archaea, 11,759 bacteria, and 200 eukaryotic taxa, we show how enzyme functions form universality classes with common scaling behavior in their relative abundances across the datasets. We verify that these scaling laws are not explained by the presence of compounds, reactions, and enzyme functions shared across known examples of life. We demonstrate how these scaling laws can be used as a tool for inferring properties of ancient life by comparing their predictions with a consensus model for the last universal common ancestor (LUCA). We also illustrate how network analyses shed light on the functional principles underlying the observed scaling behaviors. Together, our results establish the existence of a new kind of biochemical universality, independent of the details of life on Earth's component chemistry, with implications for guiding our search for missing biochemical diversity on Earth or for biochemistries that might deviate from the exact chemical makeup of life as we know it, such as at the origins of life, in alien environments, or in the design of synthetic life.

Criticality Distinguishes the Ensemble of Biological Regulatory Networks.

The hypothesis that many living systems should exhibit near-critical behavior is well motivated theoretically, and an increasing number of cases have been demonstrated empirically. However, a systematic analysis across biological networks, which would enable identification of the network properties that drive criticality, has not yet been realized. Here, we provide a first comprehensive survey of criticality across a diverse sample of biological networks, leveraging a publicly available database of 67 Boolean models of regulatory circuits. We find all 67 networks to be near critical. By comparing to ensembles of random networks with similar topological and logical properties, we show that criticality in biological networks is not predictable solely from macroscale properties such as mean degree ⟨K⟩ and mean bias in the logic functions ⟨p⟩, as previously emphasized in theories of random Boolean networks. Instead, the ensemble of real biological circuits is jointly constrained by the local causal structure and logic of each node. In this way, biological regulatory networks are more distinguished from random networks by their criticality than by other macroscale network properties such as degree distribution, edge density, or fraction of activating conditions.

Experiments with LDA and Top2Vec for embedded topic discovery on social media data-A case study of cystic fibrosis.

Social media has become an important resource for discussing, sharing, and seeking information pertinent to rare diseases by patients and their families, given the low prevalence in the extraordinarily sparse populations. In our previous study, we identified prevalent topics from Reddit via topic modeling for cystic fibrosis (CF). While we were able to derive/access concerns/needs/questions of patients with CF, we observed challenges and issues with the traditional techniques of topic modeling, e.g., Latent Dirichlet Allocation (LDA), for fulfilling the task of topic extraction. Thus, here we present our experiments to extend the previous study with an aim of improving the performance of topic modeling, by experimenting with LDA model optimization and examination of the Top2Vec model with different embedding models. With the demonstrated results with higher coherence and qualitatively higher human readability of derived topics, we implemented the Top2Vec model with doc2vec as the embedding model as our final model to extract topics from a subreddit of CF ("r/CysticFibrosis") and proposed to expand its use with other types of social media data for other rare diseases for better assessing patients' needs with social media data.