Would be interesting to extend to observations of chaos or entropy one level above each recognizable hierarchy, forcing a new organizing paradigm.

(2011)

After reading the abstract I'm not sure what they are trying to prove. None of their examples are relevant to "spontaneous" emergence of hierarchy, they are all somehow tied to environmental or economic factors.

Hierarchy is definitely useful in some cases but has interesting tradeoffs. In emergency conditions it's very useful to have a strong hierarchy (especially if the leader has experience with that type of emergency), but during 'good times' strong top-down regulation represses creativity and adaptability.

Alternating between phases of hierarchy to consolidate good ideas from phases with high generation of ideas/diversity is probably ideal, and is probably what I would have looked into if I was studying hierarchy.

I'm going to read more of the thesis to be sure, but part about VDJ recombination seems tenuous - the fact that some aspects of VDJ recombination are regulated or vary between individuals shouldn't surprise anyone since environments and diseases vary all over the world. It's also not a new finding.

Here's some better reading about the origins of antigen receptor diversity, or as some people call it, the Generation of Diversity (GOD):

Another manifestation of GOD (2004) https://www.nature.com/articles/430157a

Evolutionarily conserved TCR binding sites, identification of T cells in primary lymphoid tissues, and surprising trans-rearrangements in nurse shark (2010) https://pubmed.ncbi.nlm.nih.gov/20488795/

Evidence of G.O.D.’s Miracle: Unearthing a RAG Transposon (2017) https://pmc.ncbi.nlm.nih.gov/articles/PMC5428540/

Origin of immunoglobulins and T cell receptors: A candidate gene for invasion by the RAG transposon (2025) https://pubmed.ncbi.nlm.nih.gov/40614193/

edit, did not realize this was written by the He Jiankui, https://en.wikipedia.org/wiki/He_Jiankui#Human_gene-editing_...

Makes sense that his thesis was in biophysics, not in biology itself. in a biology department someone would probably have disillusioned him of his top-down control tendencies

For context, I think this is the same infamous

https://en.wikipedia.org/wiki/He_Jiankui

https://knowyourmeme.com/memes/people/jiankui-he

He Jiankui is better known for performing the first germ-line (i.e. inheritable by children) genome editing of humans.

Lost me at "The main theme of biology in twentieth-century is an attempt to reduce biological phenomena to the behavior of molecules". Maybe the theme of biophysics in the 80s-2000s, but certainly not all of biology. Evolution? The central dogma? The cell + DNA+ evolution is what I'd put as the main themes. At least toward the end of century in biophysics the ideas of emergence and hierarchy can be found in any biology or biophysics textbook.

Having done it myself, I really hate the apparently irresistible pull to set up a straw man of your field in the abstract/intro then saying your minor results resolve it. I guess it's part of science now, but I wish it could at least be confined to job talks(1).

Continuing "We argue here that "hierarchy" is a critical level of biological organization". Welcome to the club. Again, any biology/biophysics textbook worth its salt from the 90s on (conservatively) would include probably by page 50 a picture/discussion of the multiple scales involved and probably even mention hierarchical organization explicitly.

It's just hard to take seriously. What is he actually trying to prove/show? Searching Google scholar Im prematurely concluding he applied existing clustering methods (clustering was very sexy in statistical physics right around 2010) and found some modularity across scales. You couldn't throw a rock 10 feet in a physics/biophysics department around that time without finding someone doing some clustering study to show some modular/hierarchical structure in some biological or otherwise "complex" system (trade networks in his case).

Bah I think I'm just in a bad mood lol don't mind me.

(1) Which reminds me of one job talk I sat in (physics department) where the speaker tried to pass off levinthal's "paradox" of protein folding as unresolved until he graced the field with his brilliance. Maybe he thought no one in the department knew anything about proteins? I was almost impressed by the boldness.