The Automation of Science

Abstract

The basis of science is the hypothetico-deductive method and the recording of experiments in sufficient detail to enable reproducibility. We report the development of Robot Scientist "Adam," which advances the automation of both. Adam has autonomously generated functional genomics hypotheses about the yeast Saccharomyces cerevisiae and experimentally tested these hypotheses by using laboratory automation. We have confirmed Adam's conclusions through manual experiments. To describe Adam's research, we have developed an ontology and logical language. The resulting formalization involves over 10,000 different research units in a nested treelike structure, 10 levels deep, that relates the 6.6 million biomass measurements to their logical description. This formalization describes how a machine contributed to scientific knowledge.

Representation of research hypotheses

“…Unfortunately, this general method is too inefficient to deal with large bioinformatic models. We therefore developed an alternative approach based on using standard bioinformatic methods – these are essentially based on abductive hypothesis formations [11]. Adam uses an automated strategy based on 1) finding the enzyme class (EC number) of the missing reaction, 2) finding genes that code for this EC class in other organisms, 3) finding homologous genes in yeast.…”

“…The idea of a Robot Scientist is to combine laboratory automation, automated hypothesis formation, and other techniques from Artificial Intelligence to “close the loop” and automate the whole scientific process (see Figure 1) [11]. Adam has a -20°C freezer, 3 incubators, 2 readers, 3 liquid handlers, 3 robotic arms, 2 robot tracks, a centrifuge, a washer, an environmental control system, etc.…”

“…The proposed representation of research and negative hypotheses and its logical and textual representations are defined and tested within LABORS [11,15]. LABORS is designed to support investigations run by Adam for the area of Systems Biology and Functional Genomics.…”

“…], and the representation of structural research units is based on LABORS and DDI (an ontology for the Description of Drug Discovery investigations) [12]). Instances of the hypotheses defined in LABORS, and instances of the recorded research units, are stored in a publicly available database [11,13]. All the hypotheses discussed below have been automatically generated by the Robot Scientist “Adam” (A Discovery Machine) [14].…”

“…Our experiences in formally recording research hypotheses, and analysing automatically generated hypotheses are summarised as “lessons learned”. The examples in this paper are from the investigations run by Adam, the investigation into re-discovery of gene functions in aromatic amino acids pathway, and the investigation into novel biological knowledge, which are reported in [14] and [11]; all the information about the investigations, including procedures and data, is available at the Robot Scientist project web site [13]. …”