Has nature ever created a code?

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Sheldon's picture
"Here is an idea. Instead of

"Here is an idea. Instead of posting here on an atheist forum board, why don't you find a science forum board and post there? I would guarantee you would find your answer there."

Now that's pretty hilarious. Can you imagine...

Calilasseia's picture
Oh dear. Time to reprise this

Oh dear. Time to reprise this.

*Information* is nothing more than the observational data available with respect to the current state of a system of interest. That is IT. Two rigorous mathematical treatments of information, namely Shannon's treatment and the treatment by Kolmogorov & Chaitin, are predicated on this fundamental notion. Indeed, when Claude Shannon wrote his seminal 1948 paper on information transmission, he *explicitly removed* ascribed meaning from that treatment, because ascribed meaning was *wholly irrelevant* to the analysis of the behaviour of information in a real world system. Allow me to present a nice example from the world of computer programming.

Here is a string of data (written as hexadecimal bytes):

81 16 00 2A FF 00

Now, to an 8086 processor, this string of bytes codes for a single 8086 machine language instruction, namely:

ADC [2A00H], 00FFH

which adds the immediate value of 00FFH (255 decimal) to whatever value is currently stored at the 16-bit memory location addressed by DS:2A00H (note that 8086 processors use segmented memory addressing, with DS implied as the default segment register unless the base address is of the form [BP+disp], in which case the default segment register is SS).

However, on an older, 8-bit 6502 processor, the above sequence codes for *multiple* instructions, namely the following sequence:

CLC
ASL ($00,X)
LDX #$FF
BRK

The first of these instructions clears the carry flag in the processor status register P. The second instruction takes the operand $00, adds to it the contents of the X register (8-bit addition only), and uses that computed address (call this N) as an index into the first 256 bytes of memory (page zero). The contents of address N and address N+1 together then constitute a 16-bit pointer into another location in memory. The 8-bit contents of this location are then shifted one bit position left (ASL stands for Arithmetic Shift Left). The third instruction loads the contents of the X register with the immediate value $FF (255 decimal). The third instruction, BRK, is a breakpoint instruction, and performs a complex sequence of operations. First, it takes the current value of the program counter (PC), which is now pointing at the BRK instruction, adds 2 to that value, and pushes it onto the stack (2 bytes are therefore pushed). It then pushes the contents of the processor status register P. Then, it loads the contents of the memory locations $FFFE and $FFFF (the top 2 locations in the 6502 address space) into the program counter and continues execution from there. The top end of memory in a 6502 system typically consists of ROM, and the hard-coded value stored in locations $FFFE/$FFFF is typically a vector to a breakpoint debugging routine in ROM, but that's an implementation dependent feature, and the exact contents of $FFFE/$FFFF vary accordingly from system to system.

To make matters even more interesting, the bytes also have meaning to a Motorola 6809 processor, viz:

CMPA #$16
NEG $2AFF
NEG ??

The first instruction is "compare accumulator A with the value $16 (22 decimal)". This performs an implicit subtraction of the operand $16 from the current contents of accumulator A, sets the condition codes (CC) according to whether the result is positive, zero or negative (and also sets other bits allowing more intricate comparisons to be made) but discards the actual result of the subtraction. The next instruction, NEG $2AFF, takes the contents of the memory location at address $2AFF (decimal 11,007), and negates it (so that a value of +8 becomes -8 and vice versa, assuming 2's complement storage). The next instruction is incomplete, hence the ?? operand, because the NEG opcode (the 00 byte) needs two following bytes to specify a memory address in order to specify which memory location's contents to negate. So, whatever two bytes follow our 6-byte stream will become the address operand for this NEG instruction.

Now, that's ONE stream of bytes, which has THREE different meanings for three different processors. Therefore ascribing meaning to the byte stream as part of the process of analysing *transmission* of the data is *erroneous*. Meaning only becomes important once the data has been transmitted and received, and the receiver decides to put that data to use. If we have three different computers receiving this 6-byte stream from appropriate sources, then the Shannon information content of each bit stream is identical, but our three different computers will ascribe *totally* different meanings to the byte stream, if they are regarded as part of a program instruction sequence. An 8086-based computer will regard the byte stream as an ADC instruction, the 6502-based computer will regard it as a CLC, ASL, LDX, BRK sequence, and the 6809-based computer will regard it as a CMPA, NEG, NEG sequence (and the latter will demand two more bytes to be transmitted in order to complete the last instruction).

Consequently, ascribed meaning is wholly irrelevant to the *rigorous* treatment of information. Creationists routinely introduce the error of assuming *a priori* that "information" and "ascribed meaning" are synonymous, which the above example refutes wholesale (along with thousands of others that could be posted if I had the time). Of course, creationists conflate information with ascribed meaning *deliberately*, because they seek to expound the view that information is a magic entity, and therefore requires an invisible magic man in order to come into existence. This is complete rot, as the Shannon and Kolmogorov/Chaitin analyses of information demonstrate readily, not to mention Turing's large body of work with respect to information. All that matters, at bottom, is that the entities and interactions applicable to a given system of interest *produce different results when applied to different states of that system*. Information *sensu stricto*, namely the observational data available with respect to the current state of a system, only becomes "meaningful" when different states lead to different outcomes during appropriate interactions applicable to the system, and the only "meaning" that matters, at bottom, is *what outcomes result from those different system states*, which in the case of the computer data above, *differs from system to system*.

As a corollary of the above, all that matters, in a *rigorous* treatment, is the following:

[1] What states a physical system of interest can occupy;

[2] What interactions take place as a result of these physical states.

Indeed, this is the *entire basis* upon which Turing machines are founded. Turing machines consist, at their core, of a symbol state table, each element of which is indexed as a two-dimensional array by the symbol being read, and the current state of the machine performing the reading. Each of those elements contains the following:

[1] What symbol to replace the current symbol with at the current reading position;

[2] What movement to perform in order to change the reading position and acquire the next symbol;

[3] What state the machine should adopt after performing the above operations.

This blind, mechanical, deterministic system is the foundation upon which modern computing is built. ALL digital processors are, in effect, electronic embodiments of Turing machines, and they are manifestly physical entities - physical entities, moreover, that are capable of processing information at high speed. At bottom, all that they are doing is manipulating the flow of electrons within their semiconductor substrates, yet this manipulation of electrons allows us to perform such tasks as computing fast Fourier transforms, run simulations of everything from weather systems to military aircraft, and, for those familiar with the Isabelle suite of software, allows us to check mathematical proofs for consistency and rigour. No magic was required to put Isabelle together, all that was required was for sufficiently informed humans to work out what processes would result in the relevant end product, and instantiate that as a huge collection of bits, once again stored in an appropriate medium. The point here being that if you change the physical arrangement of that medium, you change its information content. The physical arrangement of any storage medium determines the information content of that medium. What another system does with that content, of course, is again a function of its physical constitution, and the interactions permitted by that physical constitution, which in turn leads to the conclusion that *ascribed meaning* is nothing more than the particular set of interactions arising from the physical structure of the entity ascribing the meaning. Therefore creationist attempts to conflate ascribed meaning with information fail not only for lack of rigour, but fail because at bottom, *ascribed meaning itself can be traced to a physical basis* with respect, at least, to Turing machines and any entity that can be modelled by them.

Now, Perry Marshall (a creationist who is fond of specious "information" pseudo-arguments) erects the bogus argument that DNA is a "code". This IS bogus. DNA is simply an organic molecule that is capable of existing in a large number of states, each of which results in a different outcome with respect to the chemical interactions that the molecule takes part in. Because it can exist in a large number of states, because those states are all associated with specific, systematic interactions (such as the production of a particular protein after transcription), and because those states are coupled to those systematic and well-defined interactions in a largely one-to-one manner (for the time being, I'll leave to one side complications such as selenocysteine, which were afterthoughts grafted onto the original system), they can be treated in an information-theoretic manner *as if* they constituted a "code", because doing so simplifies our understanding of those systematic interactions, and facilitates further detailed analysis of that system. That, again, is IT. The idea that DNA constitutes a "code" *intrinsically* is merely a baseless creationist assertion resulting from deliberate apologetic misrepresentation of the *code analogy*. A misrepresentation that itself is then subject to rampant discoursive misuse, because the argument erected consists of:

[1] DNA is a code (unsupported baseless assertion);

[2] All codes are produced by "intelligence" (deliberately omitting the fact that the only "intelligence" we have *evidence* of that produces codes is *human* intelligence);

[3] Therefore an "intelligence" produced DNA (the inference being that this "intelligence" is *supernatural*, which doesn't even arise as a corollary from [2] when one factors in the omitted detail, that the only "intelligence" we have *evidence* for as a code producer is *human*, and therefore *natural*, intelligence).

This argument is fatuous as it stands, even without factoring in extra scientific knowledge that has been acquired in relatively recent times, but when we *do* factor in this knowledge, it becomes absurd to the Nth degree. That scientific knowledge consists of at least eleven scientific papers demonstrating that the "genetic code" is itself an EVOLVABLE ENTITY. The eleven papers in my collection are:

A Co-Evolution Theory Of The Genetic Code by J. Tze-Fei Wong, Proceedings of the National Academy of Sciences of the USA, 72(5): 1909-1912 (May 1975)

A Mechanism For The Association Of Amino Acids With Their Codons And The Origin Of The Genetic Code by Shelley D. Copley, Eric Smith and Harold J. Morowitz, Proceedings of the National Academy of Sciences of the USA, 102(12): 4442-4447 (22nd March 2005)

Collective Evolution And The Genetic Code by Kalin Vetsigian, Carl Woese and Nigel Goldenfeld, Proceedings of the National Academy of Sciences of the USA, 103(28): 10696-10701 (11th July 2006)

Emergence Of A Code In The Polymerisation Of Amino Acids Along RNA Templates by Jean Lehmann, Michel Ciblis and Albert Libchaber, Public Library of Science One, 4(6): e5773 (DOI: 10.1371/journalpone.0005773, 3rd June, 2009)

Evolution Of Amino Acid Frequencies In Proteins Over Deep Time: Inferred Order of Introduction Of Amino Acids Into The Genetic Code by Dawn J. Brooks, Jacques R. Fresco, Arthur M. Lesk and Mona Singh, Molecular and Biological Evolution, 19(10): 1645-1655 (2002)

Evolution Of The Genetic Code: Partial Optimisation Of A Random Code For Robustness To Translation Error In A Rugged Fitness Landscape by Artem S. Nvozhilov, Yur I. Wolf and Eugene V. Koonin, Biology Direct, {b]2: 24 (23rd October 2007)

Importance Of Compartment Formation For A Self-Encoding System by Tomoaki Matsuura, Muneyoshi Yamaguchi, Elizabeth P. Ko-Mitamura, Yasufumi Shima, Itaru Urabe and Tetsuya Yomo, Proceedings of the National Academy of Sciences of the USA, 99(11): 7514-7517 (28th May 2002)

On The Origin Of The Genetic Code: Signatures Of Its Primordial Complementarity In tRNAs And Aminoacyl-tRNA Synthetases by S. N. Rodin and A. S. Rodin, Heredity, 100: 341-355 (5th March 2008)

Recent Evidence For Evolution Of The Genetic Code by Syozo Osawa, Thomas H. Jukes, Kimitsuna Watanabe and Akiro Muto, Microbiological Reviews, 56(1): 229-264 (March 1992)

Rewiring The Keyboard: Evolvability Of The Genetic Code by Robin D. Knight, Stephen J. Freeland and Laura F. Landweber, Nature Reviews Genetics, 2: 49-58 (January 2001)

A Simple Model Based On Mutation And Selection Explains Trends In Codon And Amino-Acid Usage And GC Composition Within And Across Genomes by Robin D. Knight, Stephen J. Freeland and Laura F. Landweber, Genome Biology, 2(4): research0010.1–0010.13 (22nd March 2001)

This collection of papers is *incomplete*, as more have been published in the relevant journals since I compiled this list.

So, since we have peer reviewed scientific papers demonstrating that the "genetic code" is itself an evolvable entity, and indeed, since scientists have published experimental work investigating the behaviour of alternative genetic codes arising from this research, the idea that an invisible magic man was needed for this is recrudescently nonsensical.

However, an essential concept is required to be covered in more detail here, namely, the *use of analogy to aid understanding*, Scientists generate analogies as a means of summarising interactions and entities that would, if expounded in detail, result in truly frightening levels of verbosity. Analogies are constructed for two purposes - disseminating understanding of a system of interest, and brevity. Analogies are conceptual tools we press into service to make sense of intricate systems of entities and interactions. Those analogies are NOT the systems in question, an elementary concept that is frequently discarded in a duplicitous manner by pedlars of creationist apologetics, who frequently deploy improper conflations not to enlighten, but to obfuscate in pursuit of an agenda. That concept is summarised succinctly as "the map is not the terrain" (a phrase donated to me by an acquaintance with a particularly keen eye for such matters).

Indeed, thanks to Turing and his successors in the relevant fields, we can see that *all* systems of interaction, that can be determined by observation to obey well defined rules, can be modelled by a suitably constructed Turing machine - this is, indeed what every simulation program in existence does. A simulation models the behaviour of a system of interest, by applying the well-defined rules determined to be in operation therein, and generating appropriate output, so that [1] the correlation with observational reality can be checked, and [2] to allow us to investigate, within a "sandbox" of sorts, what is likely to happen if that system is taken into regions of operation that would be impractical or dangerous to take the *real* system into. I'm reminded at this juncture, that Turing's seminal discovery can be summarised as follows: "every process in the universe can be reduced to a meaningless string of symbols", just as Gödel's Incompleteness Theorem can be summarised as "every idea in the universe can be reduced to a meaningless string of symbols", which is what he did to number theory in order to demonstrate said incompleteness. :)

It should come as no surprise, that chemistry, a discipline whose entities obey well-defined rules of interaction, to the point where chemists have been able to investigate syntheses and reactions by the million, is itself amenable to such modelling, and as a corollary, amenable to the construction of numerous analogies to facilitate understanding of those interactions. DNA, as an organic molecule, falls within this remit admirably. Not least, because particular subunits have their own well-defined interactions, and which, as a corollary, are modelable and subject to representation by analogy. The so-called "genetic code" is simply another one of those analogies, and, courtesy of the above papers (along with MANY others), has itself been demonstrated to be an entity subject to evolutionary processes. Once again, it's testable natural processes all the way down, resulting in system state changes in collections of relevant entities. That is IT. We don't need to introduce superfluous mythological entities to understand any of this, we simply need to expend diligent effort learning from antecedent biochemists.

Indeed, every time I've seen a creationist try to erect a fake "gotcha", by pointing to some gap in scientific knowledge, it transpires that either [1] the gap ends up being filled quickly by relevant research, or [2] wasn't a gap in the first place, because extant research had already answered the relevant questions. Furthermore, that research sometimes answers questions that creationists didn't even know *existed* when the research was being conducted, but which, in all too familiarly observed mendacious manner, then become co-opted into the apologetic fabrications that creationists mistakenly think enjoys the same imprimatur as real scientific research.

There are, of course other fallacies relevant to cover here, but space is limited, and it will be apposite to return to those at a later date. But for now, the key concepts to be remembered are:

[1] Information is NOT a magic entity. It is simply the data extant with respect to the current state of a system of interest.

[2] Ascribed meaning is also not a magic entity. It is simply the set of subsequent interactions that are set in motion, when the current state of a system of interest is modified by other systems of interest.

[3] That pithy phrase, "the map is not the terrain", is suitably illuminative with respect to the above.

[4] All of the above come into play, the moment *any* well defined rules of interaction exist, describing the behaviour of a system of interest.

Indeed, that is, at bottom, what science does - it examines systems of interest, determines what entities and interactions are present therein, and what well-defined rules describe the behaviour thereof. And that brings me to the other concept to take note of here - science is a DEscriptive enterprise, NOT a PREscriptive enterprise. Science works as well as it does, because it pays attention to observational data, including when said data tells us we need to *revise* our view of a system of interest, and as a consequence, DEscribes what happens, instead of attempting to PREscribe what happens. That distinction is important, because it results in the emergence of a vast canyon separating science and religion. Religion purports to declare by decree, that the universe and its contents operate in a given manner, regardless of how frequently observational reality laughs at the pretension inherent therein, whilst science lets the data determine what is being said. Another massive difference, is that religion attempts to pretend that its blind assertions constitite The Truth™, unswerving and unbending forever, regardless of how often reality says otherwise, whilst science simply says "this is our best current model, and so far, works well enough to allow us to do the following when we use it", and remains open to *changing* that model when the data tells us change is needed. The power and flexibility arising from letting the data do the talking, is one of science's greatest gifts, and one we should be openly celebrating. Not least because it also tells us, in no uncertain terms, which ideas are *wrong*.

And that's the beauty of a genuine scientific hypothesis. When constructed, a genuine scientific hypothesis is *prepared to be wrong*. It's prepared to be given short shrift by the data, once the experiments are conducted. A genuine scientific hypothesis results in *predictions* about the behaviour of the system of interest, which can be searched for, and if not found, send the authors back to the drawing board. On the other hand, if the data says that said hypothesis is in accord with observation, we've learned something special. Something that can *never* be learned from mythological assertion, because mythological assertion is upheld by fabricating excuses to hand-wave away inconvenient falsifying data, in a desperate attempt to preserve the so-called "sacred" status of the assertion. The bad news for those who think this is the way forward, is that nothing is sacred. EVERY assertion is, by definition, a free-fire zone for every bearer of discoursive miniguns to open fire at. If you don't want your precious assertions subject to such attention, don't parade them in public.

I think this covers relevant important bases.

Sheldon's picture
"And that's the beauty of a

"And that's the beauty of a genuine scientific hypothesis. When constructed, a genuine scientific hypothesis is *prepared to be wrong*. It's prepared to be given short shrift by the data, once the experiments are conducted. A genuine scientific hypothesis results in *predictions* about the behaviour of the system of interest, which can be searched for, and if not found, send the authors back to the drawing board. On the other hand, if the data says that said hypothesis is in accord with observation, we've learned something special. Something that can *never* be learned from mythological assertion, because mythological assertion is upheld by fabricating excuses to hand-wave away inconvenient falsifying data, in a desperate attempt to preserve the so-called "sacred" status of the assertion. The bad news for those who think this is the way forward, is that nothing is sacred. EVERY assertion is, by definition, a free-fire zone for every bearer of discoursive miniguns to open fire at. If you don't want your precious assertions subject to such attention, don't parade them in public."

Thank you, that nails it pretty neatly. Excellent post as well.

Grinseed's picture
@Calilasseia, that's a

@Calilasseia, that's a beautiful post, thanks. Got to read it again, but I doubt Vanderbilt will manage to stay awake for an entire one-sit reading, much less understand or appreciate what you have shared.

@J N Vanderbilt III, you asked,

"So what you’re saying virtually is that with time every thing is possible , things like getting perfect looking moths eyes on wings including fungus spots, what could be more convenient or coincidental?"

No. What I explained, had you read and understood my post about moths, is that time (hundreds of millions of years), population levels (billions), the innumerable variation provided by genetic activity produced by meiosis (i.e. division and recombination), natural and sexual selection pressures, genetic drift, mutations, gene flow and countless permutations generated by local environmental influences (i.e. temperature, humidity fluctuations) and many other factors, all lead to what Darwin referred to as 'endless forms most beautiful', and more specifically, to several thousands of species of moths and butterflies that mimic birds eyes alone.

Your nonsense about 'Lincoln pennies' is not possible as it has no bearing on evolutionary issues. Birds, lizards and spiders don't care for money.

Time is not always a prime issue. The butterfly named "Bicyclus anynana" is a popular reference for rapid adaption in butterfly markings. In Malawi, in south-east Africa, in the wet season the B. anynana will emerge from its chrysalid with large colourful eye spots to deter predators. But in the dry season, when the ground is covered with dead dry foliage, the next generation of this butterfly emerges a dull brown colour, with mere spots instead of eyes.
When the wet season eases, the temperatures cool and humidity drops, caterpillars (the period in which the wings are initially formed) sense the change primarily through hormonal responses, triggering genetic ones and the resulting butterflies all through the dry season, at rest, can look like speckled turds. When the wet season returns, the next generations resume the large eye spots.

Now detail for us how the squamata order of reptiles, or snakes, if you prefer, got their voice boxes?
Or you can just leave me the relevant bible verse if you like.

PS again this post was not for Vanderbilt's benefit, who will ignorantly discount it, if he ever regains consciousness again, after reading Calilasseia's fine post.

Calilasseia's picture
A little something for

A little something for Grinseed to enjoy here for the moment ...

I have in the collection, papers demonstrating that butterfly wing patterns arise in a manner consonant with the Turing morphogenesis hypothesis that he advanced back in 1952. Indeed, those papers cover specific reaction-diffusion equations that are applicable in cases such as Bicyclus anyana and Papilio dardanus. Sadly I can't embed the papers in this post, but I can list those in my collection, and these include:

[1] Butterfly Wings The Evolution Of Development Of Colour Patterns by Paul M. Brakefield & Vernon French, BioEssays, 21: 391-401 (1999)

[2] Conserved Developmental Processes And The Formation Of Evolutionary Novelties: Examples From Butterfly Wings by Suzanne V Saenko, Vernon French, Paul M. Brakefield & Patricia Beldade, Philosophical Transactions of the Royal Society Part B, 363: 1549-1555 (11th January 2008)

[3] Recruitment Of A Hedgehog Regulatory Circuit In Butterfly Eyespot Evolution by David N. Keys, David L. Lewis, Jane E. Selegue, Bret J Pearson, Lisa V. Goodrich, Ronald L. Johnson, Julie Gates, Matthew P. Scott & Sean B. Carroll, Science, 283:532-534 (22nd January 1999)

[4] The Evolutionary Genetics and Developmental Basis Of Wing Pattern Formation In The Butterfly Bicyclus anynana by Antonia F. Monteiro, Paul M. Brakefield & Venron French, Evolution, 48: 1147-1157 (1994)

[5] The Genetics And Evo Devo Of Butterfly Wing Patterns by Patricia Beldade & Paul M. Brakefield, Nature Reviews Genetics, 3: 442-452 (June 2002)

[6] The Relationship Between Eyespot Shape And Wing Shape In The Butterfly Bicyclus anynana A Genetic And Morphometrical Approach by Antonia F. Monteiro, Paul M. Brakefield & Vernon French, Journal of Evolutionary Biology, 10: 787-802 (1997)

[7] A Model For Colour Pattern Formation In Papilio dardanus by Toshio Sekimura, Anotida Madzvamuze, Andrew J. Wathen & Philip K. Maini, Proceedings of the Royal Society of London Part B, 267: 851-859 (7th February 2000)

[8] A Predictive Model For Colour Pattern Formation In The Butterfly Wing Of Papilio dardanus by Anotida Madzvamuze, Philip K. Maini, Andrew J. Wathen & Toshio Sekimura, Hiroshima Mathematical Journal, 32(2): 325-336 (2002)

[9] Hybrids And Hybridity by Cyril A. Clarke, Journal of the Royal Society of Medicine, 77: 821-829 (October 1984) [Special note applicable to this paper)

[10] Colour Pattern Specification In The Mocker Swallowtail Papilio dardanus The Transcription Factor Invected Is A Candidate For The Mimicry Locus H by Rebecca Clark, Sarah M. Brown, Steve C. Collins, Chrius D. Jiggins, David G. Heckel & Alfried P. Vogler, Proceedings of the Royal Society of London Part B, 275: 1181-1188 (19th February 2008)

[11] Comparative Genomics Of The Mimicry Switch In Papilio dardanus by Martijn J. T. N. Timmermans, Simon W. Baxter, Rebecca Clark, David G. Heckel, Heiko Vogel, Steve Collins, Alexie Papanicolaou, Iva Fukova, Mathieu Joron, Martin J. Thompson, Chris D. Jiggins, Richard H. Ffrench-Constant & Alfried P. Vogler, Proceedings of the Royal Society Part B, 281: 20140165 (14th May 2014)

[13] Macroevolutionary Shifts Of WntA Function Potentiate Butterfly Wing Pattern Diversity by Anyi Mazo-Vargas, Carolina Concha, Luca Livraghi, Darli Massardo, Richard W. R. Wallbank, Linlin Zhang, Joseph D. Papador, Daniel Martinez-Najera, Chris D. Jiggins, Marcus R. Kronforst, Casper J. Breuker, Robert D. Reed, Nipam H. Patel, W. Owen Macmillan & Arnaud Martin, Proceedings of the National Academy of Sciences of the USA, 114(40): 10701-10706 (3rd October 2017)

[14] Pigmentation Pattern Formation In Butterflies: Experiments And Models by H. Frederick Nijhout, Philip K. Maini, Anotida Madzvamuse, Andrew J. Wathen & Toshio Sekimura, Comptes Rendus Biologies, 326: 717-727 (21st August 2003)

[15] Pigmentation Pattern Formation In the Butterfly Wing Of Papilio dardanus by Toshio Sekimura, Anotida Madzvamuze, Andrew J. Wathen & Philip K. Maini, In: In: Mathematical Modelling and Computing in Biology and Medicine: Proceedings of the 5th European Conference for Mathematics and Theoretical Biology Conference

[16] Polymorphic Mimicry In Papilio dardanus Mosaic Dominance Big Effects And Origins b yH. Frederick Nijhout, Evolution & Development, 5(6): 579-592 (2003)

[17] Single Master Regulatory Gene Coordinates The Evolution And Development Of Butterfly Color And Iridescence by Linlin Zhang, Anyi Mazo-Vargas & Robert D. Reed, Proceedings of the National Academy of Sciences of the USA, 114(40): 10707-10712 (3rd October 2017)

[18] The Evolution Of Mimicry In The Butterfly Papilio dardanus by Cyril A. Clarke & Philip M. Sheppard, Heredity, 14: 163-173 (1960)

[19] The Evolutionary Genetics Of Highly Divergent Alleles Of The Mimicry Locus In Papilio dardanus by Martin J. Thompson, Martijn J. T. N. Timmermans, Chris D. Jiggins & Alfried P. Vogler, BMC Evolutionary Biology, 14: 140-152 (2014)

[20] The Genetics Of Some Mimetic Forms Of Papilio dardanus Brown & Papilio glaucus Linnaeus by Cyril A. Clarke & Philip M., Sheppard, Journal of Genetics, 56: 236-259 (1959)

Note that in the case of some of the papers on Papilio dardanus, these date back as far as 1959, which means that we had knowledge even then of some of the details of the genetic underpinning the emergence of the wing patterns in this butterfly. Obviously, that research has long been built upon, as the more recent papers demonstrate admirably.

By the way, a special note is applicable to paper [9] in the above list, Cyril Clarke, who was until his death in 2000, a member of my regional Entomology Society, was a long-standing expert on butterfly genetics, courtesy of his extensive experimental breeding work with Papilio dardanus, and detailed examination of the results of the crossings. However, he was also a doctor in a Liverpool hospital, situated about 45 minutes by train from my home, and during his daytime work, was assigned to the problem of Perinatal Rhesus Haemolytic Disease, which at the time resulted in serious infant mortality. His "eureka moment" came when he realised that the inheritance patterns of Rhesus Disease matched that of the inheritance of mimicry patterns in Papilio dardanus butterflies, and on the basis of this genetic discovery, was able to direct research aimed at determining the most susceptible mothers, and treating them with the then experimental gamma-globulin. It's estimated that as a result of his "eureka moment", arising from his understanding of genetics and evolutionary biology, over a million lives have been saved in the developed world since the 1960s. If you look up his citation on the pages devoted to the Lasker Award, you'll find more details about his stgory, and how his butterfly breeding experiments led to a major medical breakthrough. His paper, submitted to the Royal Society of Medicine, is probably the *only* paper submitted to a medical journal that includes an elucidation of butterfly genetics, but, lo and behold, that's how he solved the problem of Rhesus Disease.

Another win for evolutionary biology, methinks. :)

I think you'll enjoy tracking down those papers and reading their contents, and discovering just *how* much we know about butterfly wing patterns. Not that our resident creationist will bother with the actual science listed above, preferring instead his sad mythology and the lies erected to prop it up.

J N Vanderbilt III's picture
Pretty pathetic how you can’t

Pretty pathetic how you can’t come to terms with the definition of luck.
What do you think of a katydid coming to looking exactly like a leaf which benefits it?
What goes through your evotard mind?

Sheldon's picture
Please cite some worthy peer

Please cite some worthy peer reviewed publications that assert the evolution of insect camouflage involves luck.

arakish's picture
Sheldon: "Please cite some

Sheldon: "Please cite some worthy peer reviewed publications that assert the evolution of insect camouflage involves luck.
"

Sheldon, you are hoping as grand as I was about jnv3 posting on a science forum board. Just as hilarious. Just as agreeable.

Here is to hoping. Although I think it is futile.

rmfr

Grinseed's picture
@JNVIII

@JNVIII
The only pathetic issue here is your failure to understand that none of the science that reveals the astonishing complexity and beauty of the natural world attempts to disprove your god.
It only challenges the literal interpretation of your primitive bible.
As per your faith, your god created you with a superior intellect that he must have hoped you would use but he may find your flippant disregard for the breathtaking detail in his creation amounts to blasphemy and it maybe construed as an insult much worse than my atheistic wonder and reverence for the workings of nature.

arakish's picture
@ Calilasseia

@ Calilasseia

Thank you so much for those two most wonderful posts. If you don't mind, I have plagiarized them into a file for me to reference later on. Of course, I shall give attribution, so I guess it won't be true plagiarism...

rmfr

Old man shouts at clouds's picture
Seconded...Calilessia has a

Seconded...Calilessia has a file on my puter already!

Grinseed's picture
@Calilasseia, my thanks for

@Calilasseia, my thanks for your time and information. I will make the time to track down your references to add to my meagre collection of books and online material. I am no academic or even biologist, just a simple but very interested individual who tries to keep abreast of the ever increasing information that keeps incessantly flowing from scientific research.
The science aside, its stories about people like Cyril Clarke and his remarkable research achievements that prove the necessity and value of science over mythology.

J N Vanderbilt III's picture
Random mutations!, you’ve

Random mutations!, you’ve been told this a dozen times and you even know yourself that mutations are random. So when a katydid mutated to look exactly like what it needs to, with breathtaking resemblance to a leaf, what goes through your mind?

AccretedMinutiae's picture
JNV3: "Random mutations!, you

JNV3: "Random mutations!, you’ve been told this a dozen times and you even know yourself that mutations are random. So when a katydid mutated to look exactly like what it needs to, with breathtaking resemblance to a leaf, what goes through your mind?"

DNA replication is an imperfect process for many reasons - not the least of which is that it relies on entirely chemical processes that can see certain elements connecting and finishing off chains that don't exactly match the original. By the time you're looking at as complex a strand as exists in a katydid, these imperfections are sort of "built-in" to the system of reproduction... such that it is evolutionarily advantageous for there to be this sort of imperfection, because it results in diversity in the species. The differences that this diversity introduces can be slight - however if those differences are advantageous, then they propagate, while other, undesirable traits do not.

First it may have been that the "most green" of the katydid's ancestors were those eaten the least, because they blended in most with the leaves. These survivors went on to reproduce, and in their progeny there may have been variations of bumps and shapes of appendages, and the ones of these that best reproduced the look of the local flora (i.e. leaves), were the ones that again lived and went on to produce the next generation. Ultimately resulting in the creature looking just like the leaf - because those that were best able to pull of this resemblance were the ones that passed on their specific variations in the DNA onto the next generation(s).

And you want to call this "random?" As I stated, "variation" would have been proved early on to be a very worthwhile genetic trait. It provides the ability to adapt more quickly, over fewer generations. And it almost doesn't matter how slight the variations present themselves. If the creature already experiences any sort of population stability amid predators and other environmental dangers, then the best suited of those among them will shape the aspect of the future generations.

Sheldon's picture
Everyone, including me has

Everyone, including me has told YOU from the start that mutations are random, so do stop wasting everyone's time with this lie that you are telling us something we don't already know. Mutation are random and occur at a genetic level, natural selection is not random, and those mutations either are advantageous in reproducing, hence they continue, or are not and they don't. Over billions of years of incremental changes this is why we see only species that perfectly fit their environment.

"So when a katydid mutated to look exactly like what it needs to, "

Still a lie, just as it was the first time you claimed it. There is no need, either a mutation is more suited to it's environment and thus is more likely to be passed on or it is not, it has nothing to do with need or luck.

"what goes through your mind?"

Mostly I'm baffled at the sheer stupidity required for someone to blindly follow a bronze age superstition about magic apples and talking snakes, whilst denying something supported by overwhelming objective evidence based over 160 years of global scientific study. This act of yours is never going to change the facts, I can only assume you're trolling, otherwise I'm baffled as to what you hope to achieve.

Species evolution is a scientific fact, and even if it weren't, creationism would remain a superstitious myth that is entirely unevidenced. Nothing you say here will change this. Scientific facts can only be overturned by scientific evidence, and after 160+ years all the evidence supports species evolution, not one piece of scientific evidence has been validated that casts any doubt on any part of it.

Old man shouts at clouds's picture
@ JNV3

@ JNV3

So when a katydid mutated to look exactly like what it needs to

It didn't. It wasn't an overnight mutation as you seem to suggest. Take the time to watch the middle school videos we have posted, work your way up to the books Cassie linked for you.

Then if you think you still have a case for 'goddidit" come back and discuss. Leave the "what about the eyes" and "the leaf, exactly like a leaf" at the door as well as the stamping ickle feet.

Fuck me this is tedious,

Sapporo's picture
Most of this discussion is

Most of this discussion is not directly relevant to the thread question. (That's not a criticism of those who are giving @JNV3 the time of day, but the thread should have ended about 40 pages ago).

J N Vanderbilt III's picture
The time for introducing A

The time for introducing A tutorial in incremental changes that are beneficial is long over and does not apply . What you’re afraid to ponder in your mind is how randomness of mutations can exact a breathtaking replica w details, coloration, size, structure that would be the envy of an engineer trying to copy something. That’s right, RANDOMNESS is your god and you worship at the temple of LUCK

Sapporo's picture
J N Vanderbilt III: The time

J N Vanderbilt III: The time for introducing A tutorial in incremental changes that are beneficial is long over and does not apply . What you’re afraid to ponder in your mind is how randomness of mutations can exact a breathtaking replica w details, coloration, size, structure that would be the envy of an engineer trying to copy something. That’s right, RANDOMNESS is your god and you worship at the temple of LUCK

Do you always believe in things without evidence, or just pretend to?

Will you define what you mean by "nature", "created", and "code"?

Sheldon's picture
It remains a scientific fact,

It remains a scientific fact, and I remain underwhelmed by your creationist spiel. You've had the basics explained to you enough times now, deny them if you want, it won't change anything. Creationism remains a puerile unevidenced myth, and species evolution remains a scientific fact. If anyone is afraid here it is you. I have nothing to lose at all if evolution is falsified tomorrow, whereas your bias is abundantly clear.

Again please cite a single scientific paper published in worthy peer reviewed journal that claims evolution involves luck?

Calilasseia's picture
And here we see familiar

And here we see familiar creationist duplicity in action. The first part consisting of the misrepresentation of such terms as "random" and "mutation", the second part consisting of the omission of SELECTION, which is a central process in evolution.

First, let's deal with the misrepresentation of "random". As anyone who paid attention in a statistics class will already know, a *random* variable is a variable whose values conform to a *probability distribution*. Which means that already, there exist *constraints* on the permissible values that variable can take. Probability distributions occur whenever an observable quantity is capable of taking a range of values, but without an obviously deterministic process in place selecting those values. As a corollary, stating that an entity behaves in a manner consonant with the existence of a random variable, implies *by definition* that a probability distribution is applicable thereto, and therefore, that said variable is subject to the constraints applicable to the probability distribution in question. Of course, a full and *rigorous* treatment of this subject would require us to delve in depth into such topics as Markov Chains, which is beyond the scope of my post, but which anyone interested can find out about upon applying the relevant search diligence. Suffice it to say, that the mathematical analysis of random variables, and the associated probability distributions, has been on a rigorous footing for the best part of a century, and no one aware of the developments contests this.

Second, we come to the reason for that variation within the probability distribution. We may have in existence, a situation in which *numerous* well-defined testable natural processes can drive the appearance of a particular outcome, but we lack the abilty to determine before the fact, *which* of those well-defined testable natural processes actually operated, and what outcome arose as a result. Even after the fact, we may be limited by practical considerations, with respect to the data we can extract from the system, telling us which process operated to produce the outcome, particularly if that outcome is derivable from the operation of *several* of the processes in our set of applicable processes. In short, in the world of science, "random" is a shorthand for "we know which testable natural processes can produce the outcomes we see, but we don't have the data telling us which ones actually occurred". As a corollary, the outcome is modelled by a statistical random variable with an associated probability distribution, and all the relevant mathematics becomes applicable thereto.

Now, the essential point to make here, is that scientists have already documented a range of chemical reactions, that can result in mutations in DNA. There are dozens of these, and a fair number of relevant reagents able to take part in those reactions are already present in every known biological system. What remains unknown, courtesy of the technical difficulties in obtaining the data, is *which* of those reagents got to work in a given instance. Consequently, when a biologist talks about "random" mutations, this is actually a shorthand for "we know that one of these well-defined processes took place, courtesy of our experimental demonstrations of these processes producing this result, but we don't know WHICH of these processes applied". Additionally, our ability to narrow the time frame within which the event took place is also limited by practical considerations (such as the relevant ancestors being long dead). But, the fact that *experiments have been conducted* determining which chemical reactions result in which mutations, and that those experiments provide a basis upon which to determine what happened in the past, even if we're walled off from some of the fine details, means that scientists are already in a position to say much about the process.

Furthermore, the millions of controlled breeding experiments that have been conducted over the past century or so, along with the exquisitely detailed documentation thereof by the experimenters in question, provide us with a wealth of information about the nature of inheritance, that would have been a source of wonder to our forebears. That exquisitely detailed exposition of inheritance, teased out over the past century by those long, arduous experiments, allow us to determine with a high degree of certainty, what inheritance trajectory a population has taken from the past, and furthermore, in combination with molecular phylogeny (a discipline that would not even *exist* if creationist assertions were something other then ex recto fabrications), scientists can "rewind the clock", and provide a robustly plausible reconstruction of the ancestral state leading to the present. Courtesy of the fact that those arduous breeding experiments, starting from a known state, and then examining the future state of the population, allow us to determine which development paths are feasible, and which not.

So, even before a modern scientist embarks upon any experiments in the field, there already exists a wealth of prior art to build upon - another of those aspects of the scientific enterprise that is deliberately avoided by pedlars of duplicitous apologetics.

Of course, learning about that prior art takes time, and that's one of the reasons it takes time to train good scientists - they have to understand how their antecedents operated, where those antecedents scored, and where those antecedents made mistakes along the way. All the better to avoid repetition of said mistakes in the future, and build upon the successes in a more robust manner, which, strangely enough, is what evolution does - generate new variations, discard the abject failures, and build upon the competent remains.

And having introduced that nice aphorism, it's time to introduce that word much avoided by pedlars of mendacious apologetic fabrications - *selection*.

The moment a mutation appears that happens to be *selectable*, then selection goes to work. The agent of selection can be anything from predators, through choosy potential mates, to weather. Any natural process in the biosphere that differentiates between members of a population on the basis of their inheritance, constitutes a selection process, and there are a lot of these to choose from in any given instance. The point to be made here, in the interest of destroying another duplicitous creationist fabrication, is that selection isn't about "perfection": no, it's merely about *sufficient competence*. A novelty that gives an organism a slight advantage in terms of leaving offspring behind will do that, even if that novelty is crude and undeveloped. Indeed, a scientist by the name of Hugh Ford, conducted experiments, demonstrating that in the case of aposematism (warning colouration), even a bad mimic of a distasteful model will have enough of an advantage to leave more descendants behind - the paper in question is this one:

The Degree Of Mimetic Protection Gained By New Partial Mimics by Hugh A. Ford, Heredity, 27:227-236 (1971)

The same principle applies to other novelties - the moment a novelty is selectable, even if it is crude and undeveloped at the beginning, and only offers a small advantage, that advantage will duly materialise. Once that novelty becomes more and more a standard part of the population's inheritance repertoire, it becomes the foundation upon which development and refinement of that novelty can occur, so that any appearance of a more refined and better variation upon that foundation, is again subject to the same rules of advantage. Consequently, incremental steps can take us from a crude but slightly advantageous beginning, to a much more refined and developed descendant many generations down the line. Denying this elementary principle is akin to asserting that stairs can exist, but a staircase cannot.

And indeed, in the case of mimetic colouration, I was recently treated to a gem of a paper, namely this one:

Gradual And Contingent Evolutionary Emergence Of Leaf Mimicry In Butterfly Wing Patterns by Takao K. Suzuki, Schuchiro Tomita and Hideki Sezutsu, BMC Evolutionary Biology, 14: 229-241 (2014)

Full paper downloadable from:

https://bmcevolbiol.biomedcentral.com/track/pdf/10.1186/s12862-014-0229-5

In this paper, the authors demonstrate that there exist a number of well-defined steps, by which the standard wing pattern of Nymphalid butterflies, can undergo incremental changes one after the other, starting from a "standard" initial pattern, and via those incremental changes, result in the emergence of the exquisite leaf mimicry seen in butterflies of the Genus Kallima. The paper opens thus:

[QUOTE]

Results: In this study we show the evolutionary origin and process for the leaf pattern in Kallima (Nymphalidae) butterflies. Using comparative morphological analyses, we reveal that the wing patterns of Kallima and 45 closely related species share the same ground plan, suggesting that the pattern elements of leaf mimicry have been inherited across species with lineage-specific changes of their character states. On the basis of these analyses, phylogenetic comparative methods estimated past states of the pattern elements and enabled reconstruction of the wing patterns of the most recent common ancestor. This analysis shows that the leaf pattern has evolved through several intermediate patterns. Further, we use Bayesian statistical methods to estimate the temporal order of character-state changes in the pattern elements by which leaf mimesis evolved, and show that the pattern elements changed their spatial arrangement (e.g., from a curved line to a straight line) in a stepwise manner and finally establish a close resemblance to a leaf venation-like appearance.

Conclusions: Our study provides the first evidence for stepwise and contingent evolution of leaf mimicry. Leaf mimicry patterns evolved in a gradual, rather than a sudden, manner from a non-mimetic ancestor. Through a lineage of Kallima butterflies, the leaf patterns evolutionarily originated through temporal accumulation of orchestrated changes in multiple pattern elements.

[END QUOTE]

The determined order of emergence of features is presented in more detail on page 8 of that paper.

Now, combine that paper, with the various papers on the genetics of butterfly wing patterns (see my previous list of 20 papers on the subject), and we have the foundations of a comprehensive understanding of the topic. Indeed, those other papers point to the existence of definable patterning and painting genes, the patterning genes determining the spatial layout of the pattern elements, the painting genes determining which colours are applied to which pattern elements in the layout.

So, the idea that leaf mimicry is some sort of magic phenomenon, requiring an imaginary magic man to perform, is pretty much tossed into the bin by this research.

I invite the usual audience to enjoy the above finding. :)

Old man shouts at clouds's picture
@ Calilasseia

@ Calilasseia

I LIKE you! Thanks for that I actually understood it! *does a little dance*

Calilasseia's picture
Oh, by the way, one of the

Oh, by the way, one of the researchers involved in butterfly wing pattern analysis and the elucidation of the underlying mechanisms, is H. Frederick Nijhout, who happens to have written a 322 page book on the subject. Those with the funds to buy said work can find it here:

https://www.penguinrandomhouse.com/books/231773/the-development-and-evol...

From that web page:

[QUOTE]

Integrating the results of comparative morphology, experiments on pattern development, the genetics of color patterns, and theoretical modeling of pattern formation, Nijhout shows that the enormous diversity of natural patterns arises largely from quantitative variations in a small set of readily understandable generating rules.

[END QUOTE]

More on this as I delve further into the topic. :)

Calilasseia's picture
Meanwhile, another gem of a

Meanwhile, another gem of a paper has just crossed my path, namely this one:

Wingless And Aristaless2 Define A Developmental Ground Plan For Moth And Butterfly Pattern Wing Evolution by Arnaud Martin & Robert D. Reed, Molecular & Biological Evolution, 27(12): 2864-2878 (12 July 2010)

Full paper downloadable from here:

https://watermark.silverchair.com/msq173.pdf?token=AQECAHi208BE49Ooan9kk...

The paper opens with this:

[QUOTE]

Butterfly wing patterns have long been a favorite system for studying the evolutionary radiation of complex morphologies. One of the key characteristics of the system is that wing patterns are based on a highly conserved ground plan of pattern homologies. In fact, the evolution of lepidopteran wing patterns is proposed to have occurred through the repeated gain, loss, and modification of only a handful of serially repeated elements. In this study, we examine the evolution and development of stripe wing pattern elements. We show that expression of the developmental morphogen wingless (wg) is associated with early determination of the major basal (B), discal (DI and DII), and marginal (EI) stripe patterns in a broad sampling of Lepidoptera, suggesting homology of these pattern elements across moths and butterflies. We describe for the first time a novel Lepidoptera-specific homeobox gene, aristaless2 (al2), which precedes wg expression during the early determination of DII stripe patterns. We show that al2 was derived from a tandem duplication of the aristaless gene, whereupon it underwent a rapid coding and cis-regulatory divergence relative to its more conserved paralog aristaless1 (al1), which retained an ancestral expression pattern. The al2 stripe expression domain evolutionarily preceded the appearance of the DII pattern elements in multiple lineages, leading us to speculate that al2 represented preexisting positional information that may have facilitated DII evolution via a developmental drive mechanism. In contrast to butterfly eyespot patterns, which are often cited as a key example of developmental co-option of preexisting developmental genes, this study provides an example where the origin of a major color pattern element is associated with the evolution of a novel lepidopteran homeobox gene.

[END QUOTE]

So we now have the first insights into the genetic basis for Lepidoptera wing ground plans. Which, when combined with the other papers I've previously cited, means that we know a hell of a lot about the underlying testable natural processes generating Lepidoptera wing patterns. That paper above is a tour de force with respect to the underlying genetics, covering numerous signalling pathways implicated in the development of butterfly wing patterns, and given that homologous genes exist in other insect Orders, it would be no surprise to learn that wing patterns in other insects were found to be driven by similar mechanisms.

Sheldon's picture
Three more excellent posts.

Three more excellent posts.

Please keep these coming, and thanks. As a bumbling layman I have tried for weeks to make our creationist poster understand that his perception of random mutations and environmental variants combining to drive evolution as "luck" is inaccurate, as it ignores the real probability of the outcomes.

Sadly when you're dealing with someone who will accept on faith alone that snakes can talk, and humans be created in an instant using inexplicable magic and clay, it's near impossible to reach them with facts and evidence. Duplicitous is a very good word for this poster though.

Again please keep the excellent posts coming, it's a nice change of speed.

Old man shouts at clouds's picture
@ JNV3

@ JNV3

See? this how you debate...not stamping of feet and repetition. If you are good you can stay at the table and catch some crumbs of knowledge. Now, wipe the drool of your chin and pay attention.

arakish's picture
***tree rumbles quickly from

***tree rumbles quickly from forest, jumps onto the stone dais, begins dancing and shaking branches like pom poms***

Go Cali!

Go Cali!

Go Cali!

He's our guy.

Go Cali!

You go dude!

rmfr

EDIT: changed gender reference

Calilasseia's picture
Psst. I'm male. :)

Psst. I'm male. :)

arakish's picture
@ Cali

@ Cali

Oops. Sorry. That is what I get for not checking the profile. Sorry about that dude. I'll change it.

rmfr

Old man shouts at clouds's picture
@ Cali

@ Cali

"Psst Im male: "

Ok arakish back to the forest, I made the same mistake *hides bouquet and shiny apple from view* see ya! *breaks into a run....* Ma ma I need some cigars!

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