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Functional information vs. classical information: Two mistakes

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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?

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LocalMinimum @36 You sound like a fellow video game developer. Phinehas
Dionisio: Good luck, friend. I'm useless against deadlines; feature creep is a fatal disease I can't live without. So, while I can advise no further, I will pray for your success. LocalMinimum
LocalMinimum @36: Thank you for all those nice tips! Will keep them in mind. The pressure is mounting up and the time is flying fast. I'm in a stage transition within the project tasks, which allows me to digress a little for while, but soon I may have to roll up the sleeves and get to work harder. Then I won't have as much time to chat here as I have these days. Also the gathering of biology papers for the scenarios might be put on pause for a some time. Dionisio
Would be nice to start with a logical-only simulation and then proceed to do graphics. I want to do a simulation of genetics and random mutation but still need to learn more about genetics (I'm a senior software engineer) But anyway.... I have some questions about evolution and information I hope to address with a genetic algoritm. Seems to me that the current evolutionary algoritms are presupposing a lot of things and they don't provide a valid argument for the origin of meaningful information based on random mutation or entropy reduction. (some people like to argue that a genetic algoritm based on random mutation and multiplication is an argument for materialism.... that's just silly) kurx78
Dionisio, Eric, kurx: thanks again for the references. My other little project has gotten a bit sticky, so it looks like I'm going to be behind on this front for a little while. I'm going to keep this post at the top of my reading list, though. Dionisio: The simulation sounds like a very worthy project. I'd offer that the trick is to avoid the path of least resistance by separating the learning aspect from the entertainment. This is the error that turns things into "edutainment". There are games nowadays that actually combine engineering with the game itself: RoboCraft, Siege, Crossout, etc. They all let you build machines from basic pieces to take on challenges. I realize you have to work with existing biology and atomizing its components for full scale simulation is currently a practically impossible task; and you may not have the time and resources to develop a full-on game mode; but I think the key is giving people a chance to dig. Even if you turned it into a puzzle with static solutions, it'll snag them a bit harder. Just remember: pleasing visual effects and soothing sound cues. Time attacks and high scores might not be a terrible idea, either, depending on what you can afford to build. LocalMinimum
Eric Anderson @33 & @34: Valid points. Thanks. I like the very first comment posted following your OP in the thread you linked to:
Moose Dr: "I think that information is the wrong metric. I think that meaning is the point. As long as we keep talking about information, rather than meaning, I think we’ll be playing loop-de-loop with the loopies forever."
Here's a link that was posted by another person in that discussion thread that you referred to @34: http://posterwall.com/blog_attachment.php?attachmentid=4573&d=1318295130 It should point to a PDF file. Interesting that the last comment posted @37 in that thread is by gpuccio saying that he could not retrieve the PDF from the given link posted @25 in that thread. Apparently I never saw that last comment GP wrote until now. My apologies for being so unthoughtful. I'm sure gpuccio forgives me that mistake. Dionisio
LocalMinimum, some good suggestions from Dionisio and kf. If you want some more homework easily accessible right from these very pages, in particular about the concept of information and the Shannon metric, may I humbly suggest: https://uncommondesc.wpengine.com/design-inference/intelligent-design-basics-information-part-iv-shannon-ii/ Look at the first three links referenced therein, in order, and then read Part IV. Best, Eric Anderson
kurx78 @25: Why would Schneider be unable to understand complex specified information? And on what basis, we must ask, does he claim such can arise via "evolution through natural selection?" Apparently he doesn't understand either of these issues. Eric Anderson
kairosfocus @30:
This ghost refuses to be exorcised by mere rhetoric.
Yes, that seems like the reality of this world. Dionisio
Another example of complex functional specified information: Live imaging of stem cells: answering old questions and raising new ones Sangbum Park, Valentina Greco, Katie Cockburn Differentiation and disease Current Opinion in Cell Biology Vol.43:30–37, doi:10.1016/j.ceb.2016.07.004
Stem cells are essential for both tissue maintenance and injury repair, but many aspects of stem cell biology remain incompletely understood. Recent advances in live imaging technology have allowed the direct visualization and tracking of a wide variety of tissue-resident stem cells in their native environments over time. Results from these studies have helped to resolve long-standing debates about stem cell regulation and function while also revealing previously unanticipated phenomena that raise new questions for future work.
They ain't seen nothin' yet. Work in progress... stay tuned. Complex complexity. Dionisio
F/N: Ponder search challenge in large config spaces and why isolated islands of configuration-based functionality make better sense than the implied alternatives of successful blind search for a golden search [that lands one on a beach-head of function right away] and/or a vast continent of incrementally improve-able function, esp. across the world of life. Where, no, saying "big numbers" with sufficient sarcasm does not make the issue conveniently go away. This ghost refuses to be exorcised by mere rhetoric. KF kairosfocus
#28 error correction: The word 'issue' was misspelled: "But as I said above, their sue is not with me, but [...]" "But as I said above, their issue is not with me, but [...]" Dionisio
kurx78 @25: FYI- Paul the Apostle wrote in his first letter to the Corinthians that God would use nobodies like me to humble those with grandiose worldly-respected degrees of any kind. IOW, our Creator can use me to sweep and mop the floor with Dr. Thomas D. Schneider's opinion on the comments @27 or on anything else for that matter, as it happened a couple of years ago with the poor knowledge shown here by a distinguished Canadian biochemistry professor. Please, note that those folks know* much more biology than what I could learn the rest of my life, but their knowledge is ridiculously insignificant compared to the knowledge of our common Maker, and it's insufficient to explain many things in biology today, including the issues presented @27 and many more described in research papers referenced in the discussion threads "Mystery at the heart of life" and "A third way of evolution?". I respect those scientists' academic and scientific credentials and wish I could know at least a fraction of what they know about biology. But as I said above, their sue is not with me, but with the Creator. I have good friends who are biology research scientists in European universities and enjoy hearing about the difficult and important work they do. I could learn a lot of biology from Dr. Thomas D. Schneider and other scientists who would like to share part of their vast knowledge of biology. But they should be willing to answer my questions on the discussed subjects too. (*) in case someone doesn't know the mentioned scientist, here's some information: https://schneider.ncifcrf.gov/schneider.html Dionisio
Scientists don't know exactly how morphogen gradients are formed and interpreted. Work in progress... not there yet. But we want to know more. That's why we look forward with increasing anticipation to reading future research papers on the subject. Because the more they find out, the more complex the complexity of biological systems turns. The complex complexity is becoming more complex with every discovery. Morphogen gradients represent a very elaborate choreography of complex functional specified information. More details are coming out of research on the different factors that determine the relative location of the morphogen sources, their production rate, the timing for their individual activation/deactivation, the morphogen degradation mechanisms, the multiple morphogen transport variants, the type of morphogen in every scenario, the interpretation of the gradients and their effect on cell fate determination, morphogenesis and organogenesis. Can anyone present a comprehensive, coherent, spatiotemporal, fully guided pathway to form those morphogen gradients so that they can be interpreted correctly in order to determine the precise fate for every cell? I'm not aware of anything like that in scientific or technological literature at any level. Now, can such a complexity be produced by unguided mechanisms? How? The answer is silence. The politely dissenting interlocutors don't seem to know what they're talking about. They better get serious and approach science with more respect. Forget Shannon, Turing, and their cousins. They can only provide partial limited reductionist explanations to complex phenomena, leaving many outstanding questions unanswered and raising new questions. We're dealing with real stuff here. Sadly we see too many folks --blindly confused-- barking up the wrong trees. Poor things. Let's show compassion to them. But let's remind them to stay on the sideline and watch in awe what the future discoveries will reveal. We ain't seen nothin' yet. The best discoveries are yet to come. Fasten your seatbelts. The ride has just started. And yes, let's persuade more students to pursue STEM careers, but specially Biology-related research. They won't find anything more fascinating within science these days. Dionisio
Definition of complex according to Merriam-Webster dictionary:
composed of two or more parts : composite hard to separate, analyze, or solve
Definition of functional
of, connected with, or being a function used to contribute to the development or maintenance of a larger whole designed or developed chiefly from the point of view of use
Definition of specify (in relation to specified):
to name or state explicitly or in detail to include as an item in a specification
Definition of specific (in relation to specified):
sharing or being those properties of something that allow it to be referred to a particular category restricted to a particular individual, situation, relation, or effect
Definition of information:
the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something […] that produce specific effects
Dissecting Dembski's "Complex Specified Information" by Thomas D. Schneider https://schneider.ncifcrf.gov/paper/ev/dembski/specified.complexity.html "So what was Dembski's mistake? It was that he proposed that the design by necessity had to come from outside the living things, whereas it comes from within them and between the organism and its environment! Normally this is called evolution by natural selection." An interesting refutation to Specified Complexity in Information (Complex information is generated by living things and environment thanks to natural selection and mutation) kurx78
Did my comments make this thread too serious? Or too boring? :) Dionisio
Did I shutdown this thread? :) Dionisio
Isn't "functional information" at the core of the ID proposition? Isn't this topic interesting to others? Did I post "off topic" comments that shutdown or at least detoured the discussion? Did I take over this thread? Sorry, didn't mean it that way. Dionisio
Here's another example of complex functional specified information being processed within the biological systems that can't be easily quantified. "Tissue patterning, through the concerted activity of a small number of signaling pathways, is critical to embryonic development." "While patterning can involve signaling between neighbouring cells, in other contexts signals act over greater distances by traversing complex cellular landscapes to instruct the fate of distant cells." Control of signaling molecule range during developmental patterning Scott G. Wilcockson, Catherine Sutcliffe, Hilary L. Ashe DOI: 10.1007/s00018-016-2433-5 Cellular and Molecular Life Sciences June 2017, Volume 74, Issue 11, pp 1937–1956 Dionisio
Here's another one: "Cell polarization is a key step in the migration, development, and organization of eukaryotic cells, both at the single cell and multicellular level. Research on the mechanisms that give rise to polarization of a given cell, and organization of polarity within a tissue has led to new understanding across cellular and developmental biology. In this review, we describe some of the history of theoretical and experimental aspects of the field, as well as some interesting questions and challenges for the future." https://www.researchgate.net/publication/316040234_Mechanisms_of_Cell_Polarization led to new understanding ? some interesting questions and challenges for the future? ? Dionisio
There's plenty of functional information implied by all the above mentioned papers, but they all leave unanswered questions and raise new ones. Dionisio
LocalMinimum, "The study of multicellular development is grounded in two complementary domains: cell biomechanics, which examines how physical forces shape the embryo, and genetic regulation and molecular signalling, which concern how cells determine their states and behaviours. Integrating both sides into a unified framework is crucial to fully understand the self-organized dynamics of morphogenesis." https://www.researchgate.net/publication/312647512_A_cell-based_computational_model_of_early_embryogenesis_coupling_mechanical_behaviour_and_gene_regulation Dionisio
LocalMinimum, "...the emergence of large structures is controlled at molecular level by interactions between various signaling pathways." https://www.researchgate.net/publication/265338995_Computational_and_mathematical_methods_for_morphogenetic_gradient_analysis_boundary_formation_and_axonal_targeting Dionisio
However, the paper @15 leaves unanswered questions and may raise new ones Dionisio
LocalMinimum, Here's another attempt to explain things: Quantifying Mosaic Development: Towards an Evo-Devo Postmodern Synthesis of the Evolution of Development via Differentiation Trees of Embryos https://www.researchgate.net/publication/306043161_Quantifying_Mosaic_Development_Towards_an_Evo-Devo_Postmodern_Synthesis_of_the_Evolution_of_Development_via_Differentiation_Trees_of_Embryos Dionisio
However, the paper @13 leaves unanswered questions and may raise new ones Dionisio
LocalMinimum, In reference to your suggestion Check this out: Morphozoic, Cellular Automata with Nested Neighborhoods as a Metamorphic Representation of Morphogenesis https://www.researchgate.net/publication/311738597_Morphozoic_Cellular_Automata_with_Nested_Neighborhoods_as_a_Metamorphic_Representation_of_Morphogenesis Dionisio
LocalMinimum, The "continuous spatial automata" model seems like an interesting idea to consider. Thanks for mentioning it here. FYI - I've been gathering biology information for a project I'm working on, which includes software development for an interactive 4D animation, kind of like a computer game, but for science education (specifically biology). The "game" should include a catalog of biology cases in different scenarios or contexts. This is supposed to motivate young students to pursue STEM careers. However, it's too early to tell if it's really effective. The project has other important tasks apart from the software development. I'm working on two tasks alternatively, but things are moving very slowly on both fronts. I'm kind of slow --my reading comprehension level is rather low-- but my Leader knows me very well and graciously allows me to do things at my pace. Anyway, even at this slow pace (aprox. 20 papers/week) the collection of papers gathered in the last 3 years is quite large. When I see an interesting paper I share it here in this website. Here's an interesting quote from a professor at MIT: “Embryonic development has its own tempo—from the thumping rock beat of early cell division to something more like modern minimalism, where you have cells working together while still doing their own thing, making the music more melodious and complex. Finally, as nerves start working and sending impulses, it moves to something more syncopated and rhythmic.” Professor Hazel Sive, MIT. http://ocw.mit.edu/faculty/hazel-sive/ There is an interesting MIT online video course on developmental biology taught by professor Sive. It's very instructive. Dr Sive was the first person who told me about morphogens a few years ago. Also I recommend the 2014 Systems Biology online courses by professor Uri Alon (offered by Weizmann Institute for Science) and professor Jeff Gore (offered by MIT). Very instructive. Perhaps there are newer courses now. I have not taken time to look for them. Dionisio
Thanks everyone for the advice/references. Got some homework to do. Dionisio: Well, I'm going to have to do some research before I can speak with any confidence (or honesty) about information content, and similarly for morphogenesis; but, in my naivete I would offer that cells within morphogenesis as a whole could be modeled as continuous spatial automata. I don't know how helpful this is, because that's a pretty heavy model. LocalMinimum
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
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.pdf Dionisio
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.pdf Dionisio
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.pdf Dionisio
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
PS, This may help those needing a 101: http://www.angelfire.com/pro/kairosfocus/resources/Info_design_and_science.htm#infoissue kairosfocus
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. KF kairosfocus
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
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
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

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