Uncommon Descent Serving The Intelligent Design Community

Functional information vs. classical information: Two mistakes

Share
Facebook
Twitter
LinkedIn
Flipboard
Print
Email

From Kirk Durston at Contemplations:

The first mistake is the failure to distinguish between classical forms of information vs. functional information, and is described in a short 2003 Nature article by Jack Szostak.(2) In the words of Szostak, classical information theory “does not consider the meaning of a message.” Furthermore, classical approaches, such as Kolmogorov complexity,(3) “fail to account for the redundancy inherent in the fact that many related sequences are structurally and functionally equivalent.” It matters a great deal to biological life whether an amino acid sequence is functional or not. Life also depends upon the fact that numerous sequences can code for the same function, in order to increase functional survivability in the face of the inevitable steady stream of mutations. Consequently, Szostak suggested “a new measure of information – functional information”.

The second mistake is closely related to the first mistake discussed above. It is the belief that entropy = functional information. … More.

Of course, it is not a mistake, really. Fourth rate science teachers typically don’t understand the problem. Smart naturalists, who understand very well, keep generating confusion in order to prevent the problem from being honestly discussed.

See also: Protein families are still improbably astonishing – retraction of Matlock and Swamidass paper in order?

Follow UD News at Twitter!

Comments
However, none of this touches the functionality side of the problem. Not even close. Our dear doctor GP has pointed at this several times in this website. He has coined the term "procedures" which seems to include the concept of complex functional specified information and the spatiotemporal mechanisms that process it. The pleiotropic effects of the genetic code and the non-coding DNA/RNA have rendered the "central dogma" outdated (to say it nicely). The evo-devo literature lacks serious studies of fundamental issues, like the accurate description of the equation systems proposed @1090 in the discussion thread "A third way of evolution?" started by Denyse almost 3 years ago. Dev(d1) = Dev(ca) + Delta(d1) Dev(d2) = Dev(ca) + Delta(d2) where d1, d2 are the descendants of their common ancestor "ca". Dev(x) is the whole process of development of the biological system x. Delta(y) includes all the changes to the Dev(x) required for getting Dev(y) from Dev(x). That includes the regulatory networks, the signaling pathways, epigenetic markers, switches, and all the spatiotemporal mechanisms like the morphogen source activation, gradient formation and interpretation, the asymmetric segregation of cell fate determinants, etc. There are many papers written on the subject, but generally they are just "parole, parole, parole" as the singer Mina would have said nicely. In practical terms they are filled with void nonsense decorated with pseudoscientific hogwash, that pretends to impress the gullible masses out there. They don't answer the fundamental question for serious evo-devo research: where's the beef? (as the old Wendy's ad asked in the mid 1980s). There yet? Nope. They ain't seen nothin' yet. Still very far from that. As new discoveries are made, the big picture in biology will point more clearly to designed biological information-processing systems that nevertheless have been grossly messed up by the accursed human history since we decided to do everything Sinatra's way. Work in progress... stay tuned. Complex complexity.Dionisio
May 4, 2017
May
05
May
4
04
2017
07:53 AM
7
07
53
AM
PDT
Here goes another piece of literature picked from a myriad of research papers written on the subject: "It is estimated there are from 5±3 million (Costello et al. 2013) to 8.7±1.3 million (Mora et al. 2011) eukaryotic species on the planet, of which only 1.5–1.6 million have been described and classified (Paz & Crawford 2012)." "Identification based on morphological characters may be tenuous and time consuming (Chapple & Ritchie 2013), usually requiring consultation with an expert. In comparison, the application of data obtained from macromolecules offers more rapid and quantifiable opportunities in systematic and phylogenetic research." Uncovering the hidden biodiversity of natural history collections: Insights from DNA barcoding and morphological characters of the Neotropical genus Orthocomotis Dognin (Lepidoptera: Tortricidae) JÓZEF RAZOWSKI, VOLKER PELZ & SEBASTIAN TARCZ DOI: 10.11646/zootaxa.4250.6.3 Zootaxa 4250(6):541 · http://biotaxa.org/Zootaxa/article/view/zootaxa.4250.6.3 https://www.researchgate.net/profile/Sebastian_Tarcz/publication/315884049_Uncovering_the_hidden_biodiversity_of_natural_history_collections_Insights_from_DNA_barcoding_and_morphological_characters_of_the_Neotropical_genus_Orthocomotis_Dognin_Lepidoptera_Tortricidae/links/58f925b50f7e9ba3ba4c6339/Uncovering-the-hidden-biodiversity-of-natural-history-collections-Insights-from-DNA-barcoding-and-morphological-characters-of-the-Neotropical-genus-Orthocomotis-Dognin-Lepidoptera-Tortricidae.pdfDionisio
May 4, 2017
May
05
May
4
04
2017
07:26 AM
7
07
26
AM
PDT
Here's another paper that deals with biological information complexity from a different perspective. Capturing the complexity of biodiversity: A critical review of economic valuation studies of biological diversity Bartosz Bartkowski, Nele Lienhoop, Bernd Hansjürgens DOI: 10.1016/j.ecolecon.2015.02.023 Ecological Economics 113:1-14 "[...] biodiversity is a complex, multi-level concept, which includes genetic, species, functional, molecular and phylogenetic diversity, among others [...]" http://www.sciencedirect.com/science/article/pii/S0921800915000701 https://www.researchgate.net/profile/Bartosz_Bartkowski/publication/273071007_Capturing_the_complexity_of_biodiversity_A_critical_review_of_economic_valuation_studies_of_biological_diversity/links/55a4b96d08ae5e82ab1f4ec5/Capturing-the-complexity-of-biodiversity-A-critical-review-of-economic-valuation-studies-of-biological-diversity.pdfDionisio
May 4, 2017
May
05
May
4
04
2017
07:13 AM
7
07
13
AM
PDT
Here's an old paper that may present the biological information measuring problem from another perspective? http://www.sciencedirect.com/science/article/pii/S1476945X12000219 Here's a link to a PDF copy of the paper: https://www.researchgate.net/profile/Keith_Farnsworth/publication/235219198_Functional_complexity_The_source_of_value_in_biodiversity/links/0c9605256995d26b17000000/Functional-complexity-The-source-of-value-in-biodiversity.pdfDionisio
May 4, 2017
May
05
May
4
04
2017
06:57 AM
6
06
57
AM
PDT
LocalMinimum - if it helps, Shannon information is just proportional to a multinomial likelihood. As most of the arguments about functional information are about improbability, I think this can be a useful lens through which to view it.Bob O'H
May 4, 2017
May
05
May
4
04
2017
06:23 AM
6
06
23
AM
PDT
PS, This may help those needing a 101: http://www.angelfire.com/pro/kairosfocus/resources/Info_design_and_science.htm#infoissuekairosfocus
May 4, 2017
May
05
May
4
04
2017
03:18 AM
3
03
18
AM
PDT
News, I have sometimes found it useful to highlight that "Shannon Information" -- in effect the average info carried per symbol in a relevant set of messages -- is more or less a metric of info-carrying capacity. Functional info rises above the flat-random carrying capacity of a given alphabet of symbols or that modified by the stochastic distribution in messages (e.g. "e" is about 1/8 of normal English text) to include that messages are specifically fitted to a system so that it may function in ways depending on the particular configuration of the coded info. Or, in the case of function-rich organisation, some suitable description language can be used to specify what is needed for relevant function, e.g. in AutoCAD drawings. This latter is relevant to D's gradients just above. KFkairosfocus
May 4, 2017
May
05
May
4
04
2017
03:16 AM
3
03
16
AM
PDT
LocalMinimum, Math won't do much in some cases of complex functional specified information, like the example given @1. First let's try to understand the concept well. Then we can see how to quantify it. Gpuccio has mastered a very interesting way of quantifying information associated with protein structures, but how can we quantify the information in the morphogen gradients?Dionisio
May 4, 2017
May
05
May
4
04
2017
02:00 AM
2
02
00
AM
PDT
I've been seeing many such articles about Shannon information and the like recently. It's quickly starting to feel like I desperately need to metabolize the math behind this.LocalMinimum
May 3, 2017
May
05
May
3
03
2017
07:45 PM
7
07
45
PM
PDT
Glad you posted this. Thanks. Information --of different complexity levels-- that has to be precisely produced and reliably transmitted according to a predefined protocol that can be interpreted accurately by entities that do something very specific --of different complexity levels-- according to such received information. Undeniably we observe this abundantly within the biological systems. Morphogen gradients are just one of the myriad of examples seen in biology. Many new research discoveries are revealing more of that complex complexity. But we ain't seen nothin' yet. The most fantastic discoveries are still ahead. The party is just starting. Stay tuned.Dionisio
May 3, 2017
May
05
May
3
03
2017
12:55 PM
12
12
55
PM
PDT
1 2

Leave a Reply