ReviewFEMS microbiology reviews2009
Bacteria as computers making computers.
Review in FEMS microbiology reviews, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
33 citing papers in PubMed.
- Transition from fermentation to precision fermentation: Role in sustainable food system.Biotechnology reports (Amsterdam, Netherlands) · 2026Review
- Dynamics of genetic circuits in Pseudomonas protegens.Cell systems · 2026Article
- Integrated network pharmacology andFrontiers in molecular biosciences · 2025Article
- Evolution of Pyrrolysyl-tRNA Synthetase: From Methanogenesis to Genetic Code Expansion.Chemical reviews · 2024Review
- Biocomputation: Moving Beyond Turing with Living Cellular Computers.Communications of the ACM · 2024Article
- Programmable Biomolecule-Mediated Processors.Journal of the American Chemical Society · 2023Review
- Monitoring the advancements in the technology of artificial cells by determining their complexity degree: Hints from complex systems descriptors.Frontiers in bioengineering and biotechnology · 2023Article
- Formalising the Pathways to Life Using Assembly Spaces.Entropy (Basel, Switzerland) · 2022Article
- Missing Links Between Gene Function and Physiology in Genomics.Frontiers in physiology · 2022Article
- Genomic Intelligence as Über Bio-Cybersecurity: The Gödel Sentence in Immuno-Cognitive Systems.Entropy (Basel, Switzerland) · 2021Article
- Contextual dependencies expand the re-usability of genetic inverters.Nature communications · 2021Article
- Omnipresent Maxwell's demons orchestrate information management in living cells.Microbial biotechnology · 2019Article
- The Hidden Charm of Life.Life (Basel, Switzerland) · 2019Article
- The Synthetic Microbiology Caucus: from abstract ideas to turning microbes into cellular machines and back.Microbial biotechnology · 2019Article
- High-Performance Biocomputing in Synthetic Biology-Integrated Transcriptional and Metabolic Circuits.Frontiers in bioengineering and biotechnology · 2019Article
- Is Research on "Synthetic Cells" Moving to the Next Level?Life (Basel, Switzerland) · 2018Article
- Evolutionary tinkering vs. rational engineering in the times of synthetic biology.Life sciences, society and policy · 2018Article
- Elastic Multi-scale Mechanisms: Computation and Biological Evolution.Journal of molecular evolution · 2018Article
- Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement.Microbial biotechnology · 2018Article
- From chemical metabolism to life: the origin of the genetic coding process.Beilstein journal of organic chemistry · 2017Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Various efforts to integrate biological knowledge into networks of interactions have produced a lively microbial systems biology. Putting molecular biology and computer sciences in perspective, we review another trend in systems biology, in which recursivity and information replace the usual concepts of differential equations, feedback and feedforward loops and the like. Noting that the processes of gene expression separate the genome from the cell machinery, we analyse the role of the separation between machine and program in computers. However, computers do not make computers. For cells to make cells requires a specific organization of the genetic program, which we investigate using available knowledge. Microbial genomes are organized into a paleome (the name emphasizes the role of the corresponding functions from the time of the origin of life), comprising a constructor and a replicator, and a cenome (emphasizing community-relevant genes), made up of genes that permit life in a particular context. The cell duplication process supposes rejuvenation of the machine and replication of the program. The paleome also possesses genes that enable information to accumulate in a ratchet-like process down the generations. The systems biology must include the dynamics of information creation in its future developments.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.