[FRIAM] All hail confirmation bias!

[Eric Smith]

Here is a nice example, of that onus accepted and handled clearly.

https://www.nature.com/articles/nature07749
Topic is the accretionary dependency structure in the large subunit of the ribosome.

In particular, see Fig. 2, which my image-page on chrome is showing me at this URL (don’t know if these URLs produce equivalent output for different users):
https://www.google.com/search?q=bokov+and+steinberg+ribosome&source=lnms&tbm=isch&sa=X&ved=0ahUKEwjXjfm58unhAhXKzLwKHXG5B60Q_AUIDigB&biw=1371&bih=745#imgrc=uExkhZIl02WciM:

The primitive data is a set of links between locations in folded RNA, which can be assigned a directionality that is very likely a dynamically meaningful one.  The result is a graph with directed links.  It is an empirical question whether the graph is cyclic or acyclic, with the answer being the latter.  The primitive data structure is only the acyclic graph.  However, a second question is whether the nodes in the graph admit a partial order, and if so, which sets of nodes constitute each distinct level within that order.  That question too has an answer in terms of the maximal extent to which the equivalence class defining a level can be extended, without violating the dependency structure in the underlying DAG.  Nodes in a level need not have been historically contemporaneous, but they reflect assembly conditions, as nodes at higher levels “plug into” nodes at lower levels, and thus require them to be in place.  This seems extremely likely to reflect an actual historical accretionary sequence, in which equivalence of nodes within a level quantifies the ambiguity of how they may have related in time.

Lots more has been done to extend this data to a detailed module decomposition, with or without the level post-processing.  Through all of it, the level decomposition continues to be salient, as levels by the analysis of the DAG also correspond roughly to horizons for generations of peptide structure.  See

https://watermark.silverchair.com/msx086.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAjwwggI4BgkqhkiG9w0BBwagggIpMIICJQIBADCCAh4GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMGr_TvxBlD6v5A3yIAgEQgIIB77pRGYntr9gP-GNtZajC6JIiEDLCsmZFdcSgAVoYO43dh_vul542Uzn2GyejvMgnqthKt7u3ZnQoenITwMrwvneJMWZ9n6-UlYuottaxIkpxp6lWIfiTIla83YKJqigjdIbWtQx_W2y2J2pJgAKOBdbvvTctto3COkdwh4C6VH5AARmbw0bRfaMH_gRW8IKRNw8m4Gw--SbRMDlkHqaXRY8WJlbkrN8uB-ygTiu4TL12LHhNiWlxCLH0LP3pLKPBMmBG0tKM5sMIuO2CDVltBItUIT6i91Z0q2x-l6u5yBWqPFlDfpYNok--att5kqPbtzT1H7IzZev-AsWYpq_ek2RdyHxrthXdn2rTzvhMjmUlb1JHoeJX6holXrs8j1PKzwg_pW-3wtR6cYZg3VBLM6V_cTnMlyNIMABBkyix8D9pBvq6Hj7zLWABE8Oq0nuVUH5vd0U8RVbqpF5SS1OKd2Y13BN_bq-4P7B3RKKYmoecn2SVqoYPHZBV7csmkq9duwoydMQFbcGsk8BYopz6zEti3BuZJxXa2J6YT1i1pXQNMvSTHXRKdsIntCJkSZsPRwS-q6GiM5r7BtTU9hOLZLq__67NMjBDpWUcOG7pglEYuqENH7xy4abOEoE5TusJg9aU6PE9Tj9ayBkHnIONBg
and Fig.5 within it:
https://www.google.com/search?q=bokov+and+steinberg+ribosome&source=lnms&tbm=isch&sa=X&ved=0ahUKEwjXjfm58unhAhXKzLwKHXG5B60Q_AUIDigB&biw=1371&bih=745#imgrc=HRSn_FYi9cUYDM:

It’s great when people take on small enough questions that they have time to speak in full sentences.

Eric



> On Apr 25, 2019, at 8:25 AM, uǝlƃ ☣ <gepropella at gmail.com> wrote:
> 
> 
> Our World Isn't Organized into Levels
> https://philpapers.org/rec/POTOWI?ref=mail
> 
>> In my view, our adherence to the levels concept in the face of the systematic problems
>> plaguing it amounts to a failure to recognize structure we’re imposing on the world, to instead
>> mistake this as structure we are reading off the world. Attachment to the concept of levels of
>> organization has, I think, contributed to underestimation of the complexity and variability
>> of our world, including the significance of causal interaction across scales. This has also
>> inhibited our ability to see limitations to our heuristic and to imagine other contrasting
>> heuristics, heuristics that may bear more in common with what our world turns out to
>> actually be like. Let’s at least entertain the possibility that the invocation of levels can
>> mislead scientific and philosophical investigations more than it informs them. I suggest that
>> the onus is on advocates of levels of organization to demonstrate the well-foundedness and
>> usefulness of this concept.
> 
> -- 
> ☣ uǝlƃ
> 
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