Talk:Assembly theory

Extended-confirmed-protected edit request on 17 December 2024

Change: "A paper published in the Journal of Molecular Evolution[11] concludes that "the hype around Assembly Theory reflects rather unfavorably both on the authors and the scientific publication system in general". The author[11] concludes that what "assembly theory really does is to detect and quantify bias caused by higher-level constraints in some well-defined rule-based worlds"; one "can use assembly theory to check whether something unexpected is going on in a very broad range of computational model worlds or universes"."

To: "A paper published in the Journal of Molecular Evolution[11] describes a philosphical disagreement with the authors of assembly theory."

Change: "Another paper authored by a group of chemists and planetary scientists published in the Journal of the Royal Society Interface[12] demonstrated that abiotic chemical processes have the potential to form crystal structures of great complexity — values exceeding the proposed abiotic/biotic divide of MA index = 15. They conclude that "while the proposal of a biosignature based on a molecular assembly index of 15 is an intriguing and testable concept, the contention that only life can generate molecular structures with MA index ≥ 15 is in error"."

To: "Another paper authored by a group of chemists and planetary scientists published in the Journal of the Royal Society Interface[12] suggested that abiotic chemical processes have the potential to form crystal structures of great complexity — values exceeding the proposed abiotic/biotic divide of MA index = 15 but these authors only consider theory and threshold for assembly theory index must be experimentally determined as described in this ref: https://royalsocietypublishing.org/doi/10.1098/rsif.2024.0367"

Change: "Two papers published in 2024 argue that assembly theory provides no insights beyond those already available using algorithmic complexity and Claude Shannon's information theory.[13][14]"

to: "Two papers published in 2024 argue that the calculation of the assembly index[13][14] is similar to Shannon Entropy or LZW but a recent paper demonstrates that the calculation of assembly index is in a different computational class to Shannon Entropy and LZW showing that this comparison is superficial described in this ref: https://arxiv.org/abs/2406.12176" Eriklooser (talk) 12:02, 17 December 2024 (UTC)

@Eriklooser: You need to explain why these changes are necessary and also respond to the multiple requests for you to disclose your apparent conflict of interest with regards to Cronin. SmartSE (talk) 17:08, 17 December 2024 (UTC)

Eriklooser has now been blocked for promotional editing. So I suspect no explanation will be forthcoming. —David Eppstein (talk) 19:07, 17 December 2024 (UTC)

The first proposed edit makes the text less informative and tries to handwave away criticism. The second proposed edit is some combination of WP:SYNTH and special pleading. The third relies on a non-peer-reviewed source and presents the AT proponents' response to criticism as definitive, which violates policy (WP:NPOV), guidelines (WP:SPS), and baseline norms of academic integrity. XOR'easter (talk) 19:59, 17 December 2024 (UTC)

Confusing sentence

I find the following sentence from the article extremely confusing. It's very long, and it contains many double negatives. I recommend rewriting it.

I would rewrite it myself, but I honestly don't understand what it's trying to say. The article is also locked, so I can't add a "Clarify" tag.

Here's the sentence:

"Benner argues that it is transparently false that non-living systems, and with no life intervention, cannot contain molecules that are complex but people would be misled in thinking that because it was published in Nature journals after peer review, these papers must be right."

LibreLearner (talk) 08:23, 11 January 2025 (UTC)

Support for Assembly Theory

Hello, I would like to propose a section on the philosophical, mathematical, and scientific support for Assembly Theory. This theory does not emerge in a complete vacuum. There are at least two previous papers that are predecessors, companions and in support to AT's formulation, Gregory Chaitin's "Towards a mathematical definition of Life", and Ioannis Tamvakis's "Quantifying Life". I can provide links if necessary. I think that AT is an important step into understanding Life, to the least philosophically, so we need a section like this to underlie that not at all scientists are negative to it, and connect it with its proper context in the history of theoretical biology. Deepforests (talk) 14:36, 11 April 2025 (UTC)

Do you have secondary sources that explicitly connect those two papers to Assembly theory? MrOllie (talk) 14:47, 11 April 2025 (UTC)

At the moment no but I think it is self evident they are connected. If you look at the formulations all 3 theories consider similar metrics. I would not consider how credible they are, just note in the page that they are in the same vein of philosophical approach to life. If we put this kernel in the wiki others might contribute more. Deepforests (talk) 17:52, 11 April 2025 (UTC)

Without sources we cannot include this connection. Wikipedia is not the right place to drum up support for others to follow this approach. —David Eppstein (talk) 17:58, 11 April 2025 (UTC)

Wikipedia is an encyclopedia though, and this theory needs to be placed in it's proper context, with all respect to you and your work. I think that if there is an explicit part about Criticism there should be a part as well of "support" somewhere in the text. Could this be in the main Background section? As an academic I should be able to contribute in connecting Assembly theory to other areas of information theory if there is a self-evident point to be made. Could I propose a short paragraph and we revise it here? Deepforests (talk) 13:10, 14 April 2025 (UTC)

Have a look at WP:NOR. We cannot draw this connection ourselves. MrOllie (talk) 20:53, 11 April 2025 (UTC)

Thank you for the link, indeed I was not aware of it. My proposal falls under the "Synthesis.." section from the link. All authors in the 3 theories explicitly propose quantifying life under information terms. Would it be acceptable to point this out with references from all 3 works? Deepforests (talk) 13:23, 14 April 2025 (UTC)

No. That is exactly the kind of thing that is barred by the policy on Synthesis. MrOllie (talk) 14:10, 14 April 2025 (UTC)

I am sorry, it seems that there is a certain way that we could mention the original research and avoid synthesis, as pointed out in the WP:NOR. That is, if I just point out what the primary sources have stated on the topic at hand. There will be no further elaboration on my part. Then we all should be happy. There is no blanket ban on referring to multiple authors's original work, is there? Would it be too much to ask to give a paragraph to be considered? Deepforests (talk) 17:09, 16 April 2025 (UTC)

I do not believe there is any way to mention these papers without performing synthesis - you have to perform synthesis to establish that they are related to the topic of this article at all. You can write a paragraph if you like, but I would not expect it to appear in the article without a secondary source that actually makes a connection. MrOllie (talk) 17:13, 16 April 2025 (UTC)