Year: 2022

METAPHORICAL BIAS. “Does the metaphorical nature of the way we represent upward and downward causation matter? The bias introduced by the metaphor is that there is a strong tendency to represent the lower levels as somehow more concrete. Many areas of science have proceeded by unravelling the small elements underlying the larger ones. But notice the bias already creeping in through the word ‘underlying’ in the sentence I have just written.” http://rsfs.royalsocietypublishing.org/content/2/1/55 View in LinkedIn

CENTRAL DOGMA OF MOLECULAR BIOLOGY. “The essence of the central dogma is that ‘coding’ between genes and proteins is one-way.” http://rsfs.royalsocietypublishing.org/content/2/1/55 View in LinkedIn

APPARENT GENE PRIMACY. “The sequences of DNA triplets form templates for the production of different amino acid sequences in proteins. Amino acid sequences do not form templates for the production of DNA sequences. That, in essence, is what was shown. The template works in only one direction, which makes the gene appear primary.” http://rsfs.royalsocietypublishing.org/content/2/1/55 View in LinkedIn

TEMPLATED WORLD. “So what does the genome cause? The coding sequences form a list of proteins and RNAs that might be made in a given organism. These parts of the genome form a database of templates.” http://rsfs.royalsocietypublishing.org/content/2/1/55 View in LinkedIn

READ-ONLY VERSUS READ-WRITE. “But the genome is not a fixed program in the sense in which such a computer program was defined when Jacob and Monod introduced their idea of ‘le programme génétique’. It is rather a ‘read–write’ memory that can be organized in response to cellular and environmental signals.” http://rsfs.royalsocietypublishing.org/content/2/1/55 View in LinkedIn

CELL SPECIFICITY WITH SINGLE CODE. “Which proteins and RNAs are made when and where is not fully specified. This is why it is possible for the 200 or so different cell types in an organism such as the human to make those cell types using exactly the same genome. A heart cell is made using precisely the same genome in its nucleus as a bone cell, a liver cell, pancreatic cell, etc.” http://rsfs.royalsocietypublishing.org/content/2/1/55 View in LinkedIn

GREATER THAN GENES ALONE. “The circuits for major biological functions necessarily include non-genome elements. That fact already tells us that the genome alone is far from sufficient.” http://rsfs.royalsocietypublishing.org/content/2/1/55 View in LinkedIn

DEPENDENT GENES. “The genome as ‘an organ of the cell’. And so it is. DNA sequences do absolutely nothing until they are triggered to do so by a variety of transcription factors, which turn genes on and off by binding to their regulatory sites, and various other forms of epigenetic control, including methylation of certain cytosines and interactions with the tails of the histones that form the protein backbone of the chromosomes. All of these, and the cellular, tissue and organ processes that determine when they are produced and used, ‘control’ the genome.” http://rsfs.royalsocietypublishing.org/content/2/1/55 View in LinkedIn

ABSURD PROPOSITION. “To think that the genome completely determines the organism is almost as absurd as thinking that the pipes in a large cathedral organ determine what the organist plays. Of course, it was the composer who did that in writing the score, and the organist himself who interprets it.” http://rsfs.royalsocietypublishing.org/content/2/1/55 View in LinkedIn

CATHEDERAL ORGAN. “This metaphor has its limitations. There is no ‘organist’. The ‘music of life’ plays itself, rather as some musical ensembles perform without a conductor. And, of course, the ‘organ’ varies between individuals in a species.” http://rsfs.royalsocietypublishing.org/content/2/1/55 View in LinkedIn