Has nature ever created a code?
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Bingo! There ARE tags I can use! I'm used to BBCode on other forums, so I was lamenting its absence here. :)
So instead of BBCode, I can use a set of permitted HTML tags. Gotcha. That's going to make posting a LOT more effective now I know this! :)
You got it. I am also used to BBCode. This is the only forums I visit that do not use BBCode. Just remember, the permitted HTML tags do NOT accept any attributes. At least none have for me. But with your below post, it looks you've got it.
Armed with the above knowledge, it's time for a test ... don't reply to this post, I'm just trying the features out :)
c = 2πr
If this works, I'll know what to do with future posts. All I need now is for superscript and subscript tags to be added to the list if so ...
I would not count on it. I have asked for strikethrough and the script tags. No answer from the Admins.
Meanwhile, I'll return to the question that opened this thread, by pointing out an elementary fact. The moment any reliably repeatable systematic set of interactions exist, and nature is replete with these, then those systematic interactions become immediately amenable to Turing style algorithmic representation. Hence our ability to write software to simulate chemical reactions, ecosystem behaviours, airflow over different aerofoil shapes, etc., though of course some of these involve more challenges than others. Indeed, there's an entire discipline devoted to evolutionary algorithms, namely the application of evolutionary processes to what were previously considered "design" activities. I have some interesting papers written in that field which I may bring here at some point, and they are highly illuminating with respect to the applicability of evolutionary processes to human design activities.
In the sense that any reliably repeatable system, capable of being represented as a set of formally defined entities and interactions, exists, then Nature has supplied us with a veritable cornucopia of "codes". Every well-defined systematic set of interactions that exists can be represented as a "code" of some sort by a suitably astute investigator, all the way from the interactions of particle physics upwards. All of them are Turing-representable, and on that basis, I consider the question closed.
I alluded to this once. Not in your detail. jnv3 just ignores anything and everything because he is completely brainwashed by religion. Now I just like having fun poking at him because he now ignores me after I really trashed and spanked him real hard in one post.
Now with you here, I am enjoying a new fresh look on this. Thanks bunches dude.
Calilasseia, I am enjoying your posts and references, which I am collecting, reading and storing for further study. There is a lot to work with.
You have a remarkable writing style that is easy to follow and like Old Man I am surprised I am understanding things that previously seemed obscure to me. This is great. I m learning new things, looking up new words, stretching comprehension and having a ball..."ex recto fabrication" had me laugh out loud on the bus on the way home.
Heh, I haven't even had chance to cover the really remarkable papers in the collection, such as the speciation experiment by Diane Dodd back in 1989, which can be replicated in any well equipped high school laboratory, and which establishes the validity of the basic postulates of allopatric speciation. In short, conduct this experiment properly, and in three years, you can produce a new species of fruit fly in your greenhouse. Then there's a nice paper on Heliconius butterflies in the collection, in which the authors replicated a wild speciation event in the laboratory. I'll have fun presenting that one at some point in the future. :)
Is everyone sitting comfortably? If so, this post will be a roller coaster ride many of you are going to love ...
Speciation By Hybridisation In Heliconius Butterflies by Jesús Mavárez, Camilo A. Salazar, Eldredge Bermingham, Christian Salcedo, Chris D. Jiggins and Mauricio Linares, Nature, 441: 868-871 (15th June 2006) [Full paper downloadable from here]
The authors continue with:
So, the authors begin by noting that the wing pattern of Heliconius heurippa is intermediate between that of local races of Heliconius melpomene and Heliconius cydno, and ask the question whether or not this is because Heliconius heurippa is a hybrid between individuals from those two races of Heliconius melpomene and Heliconius cydno. Suspicions that this might be the case were reinforced, when a genetic analysis demonstrated that certain genes present in Heliconius heurippa were admixtures of those found in Heliconius melpomene and Heliconius cydno, whilst the genes in question show NO such admixture in the other two species.
Moving on ...
So, the authors produced some experimental crosses, and noticed that those experimental crosses produced individuals possessing wing pattern intermediate between those of the parents. However, they didn't just produce single-generation crosses, instead, they tested the effects that would arise from multiple crossings across several generations, and the results were extremely illuminating to put it mildly! But I'm jumping the gun here a little ... let's see what the authors have to reveal to us, shall we?
Oh, now look at that for a spectacular set of results!
First of all, the authors crossed Heliconius melpomene with Heliconius cydno to produce F1 hybrids, then back-crossed the fertile males with females of each species. Back-crossing with Heliconius melpomene resulted in melpomene wing patterns reappearing, but back-crossing the F1 hybrids with Heliconius cydno to produce the F2 generation, then mating selected offspring of the F2 generation, produced individuals that were virtually identical to Heliconius heurippa!
But it gets even better. When the laboratory produced Heliconius heurippa analogues were mated to wild type Heliconius heurippa, they produced fertile offspring and the wing patterns bred true!.
These crossing experiments, as a consequence, constitute compellingly strong evidence that Heliconius heurippa resulted from a similar process occurring among hybrid butterflies in the wild. Not only did the authors reproduce the likely crossing sequence that produced Heliconius heurippa in the wild, thus providing a repeatable test of the relevant speciation mechanism, but the laboratory crosses were interfertile with the wild type Heliconius heurippa, further strengthening the hypothesis advanced by the authors.
Moving on ...
Well, at this point, one is tempted to say, QED. The authors could hardly have asked for better, could they? Not only did their laboratory crosses reproduce virtually identical Heliconius heurippa analogues, that were furthermore interfertile with wild Heliconius heurippa, but they observed hybrids in the wild that included individuals matching both the wild type Heliconius heurippa and the authors' laboratory analogues!
Not satisfied with this, however, the authors then turned their attention to the next part of the speciation process, and performed some experiments to determine if an isolating mechanism was in place, which would reinforce speciation. Let's take a look at those experiments, shall we?
So, the females of the new species, Heliconius heurippa, exhibited strong preference for other male Heliconius heurippa, with probabilities of out-crossing being 0.073 with Heliconius melpomene males and 0.022 with Heliconius cydno males. Male Heliconius heurippa again exhibited strong preference for female Heliconius heurippa, with probabilities of outcrossing being 0.1 with Heliconius melponeme and 0.44 with Heliconius cydno females. The table in the paper also demonstrates that the parent species also show strong assortative mating, though exhibit enough tendency to hybridise with each other to produce the offspring needed to generate Heliconius heurippa in the first place (hybridisation rate approximately 8%).
However, apart from mating experiments, the authors conducted some other experiments too. Let's take a look at these shall we?
So in this experiment, the authors demonstrated that visual cues are important to Heliconius heurippa, and that experimental manipulation of the wing pattern to mask certain features reduces their attractiveness as visual stimuli to mating.
Nice. The above experiments established that visual stimuli reproduce the same pattern of assortative mating behaviour even in the absence of pheromones, demonstrating that visual cues are the primary means of stimulating courtship behaviour in these butterflies, and that those visual cues exert strong effects upon mate preference, leading to the assortative mating patterns seen above.
So, the authors were able to reproduce a wild speciation event in the laboratory, produce laboratory analogues of the new species that were interfertile with wild type members of that species, and demonstrate the existence of assortative mating preferences producing a reproductive isolation barrier between the new species and the parents once the new species existed. Furthermore, this mechanism of speciation has been erected as a probable model in other well-studied groups of organisms, including those particular favourites of mine among the vertebrates, African Cichlid fishes. :)
Not difficult to tell why I like this paper so much, given my life long love affair with butterflies, but the reproduction of a wild speciation event in the laboratory pretty much seals the deal as far as this paper is concerned.
By the way, I note with interest that the two genes mentioned in that paper, namely invected and distal-less, are cited in later papers (for which I gave citations in earlier posts, incidentally) as being instrumental in wing pattern control in butterflies. Ah, don't you just love scientific consilience of this sort?
This so damned kewl. I feel like I am back in those genetics classes I took in college.
Hey, Old Man, Tin-Man. Quit cutting up in class. Pay attention. There will be a test later. ;-P
Just because I am quiet at the back of the class don't mean I are not paiing attenshun now....loving it, and Cali has an easy style that makes so much understandable...love it, love learning...see you at break Arakish...lets get AJ777's lunch money!
Heh, I haven't even got round to the wackiness of invertebrate reproduction yet. When I do, you'll have much fun imagining what happens when I drop that into the laps of various door knockers. Some of them leave skid marks after I let fly with the world of bizarre invertebrate shagging. :D
“The moment a mutation appears that happens to be *selectable*, then selection goes to work.”
That’s right, but what are the chances you’re going to get all the random mutations needed? And you are going to need coordinated ones if your final product is a mind blowing replica of a leaf with veins coloration, proper spacing, pattern and everything else to make a leaf ?
Selection is profoundly impotent w out the correct mutation
JNV3, you wrote, “That’s right, but what are the chances you’re going to get all the random mutations needed?”
1. The chances are somewhere in the realm of possible.
2. Needed? Needed for what? To look like it does? If so, see #1.
3. Have you had this discussion with any evolutionary biologists or do you stick to non-academic Internet forums?
What part of "the scientists in those papers I've presented have demonstrated this happening" did you fail to understand?
You should have read the weeks of nonsense when he claimed no one had ever witnessed macro evolution, and we tried to explain that macro evolution is part of the same process that starts at speciation, and that speciation had absolutely been observed in laboratories. I am getting a migraine just thinking about it.
I'm also baffled as to why he thinks successful mutations can't or shouldn't happen? And since successful in this context means they are replicated in living things and unsuccessful genes are not, why one earth would anyone be surprised that after billions of years only the successful genes are left that perfectly match the environments that have shaped them.
There is no "need", this again implies an end goal, and that's not how evolution works. You're looking at a point in an ongoing process that has taken billions of years to reach. When we say successful mutations, we mean mutations that give an advantage in reproducing, thus random mutations are relentlessly "selected" or rejected by natural factors, so after billions of years we only see the successful ones, not the failures. You are again assume only success after success, and this is why you're making this same mistake every single time in misunderstanding the probability of what we know see. If there are for the sake of argument a billion mutations, and one gives an advantage over the others, that would be the one that survives, because that is what we mean in this context by successful. You're reversing the process, and assuming it's a billion to one chance and must therefor be impossible, but ignoring the billion chances we started with. They're also accumulative , so each "successful" mutation adds to the previous, it can do nothing else unless the recipient becomes extinct, and this will have happened countless times as well.
And someone just went to a lot off trouble to explain and link research showing that tiny incremental changes in camouflage can provide enough of an advantage to ensure that genes survival. Do stop pretending the insects mutated all at once into something completely different, these tiny changes occur at the genetic level.
"Selection is profoundly impotent w out the correct mutation"
Natural selection means that the selection of only successful mutations, thus only they survive, thus we only see the accumulative mutations of billions of years of evolution, the failures aren't around for us to see, good grief just how many times do you need this enplaned to you?
Did you not read Cali's posts? Or did you have difficulty understanding that your arguments have been completely debunked?
If you are having comprehension difficulties again you can do two things, remove fingers from ears, stop singing La la la loudly, OR ask Cali for help.
If you don't want to do either then just admit you do not want to learn and you are only here to repeat vapid and erroneous creatard rubbish without thought or the desire to learn.
Time, methinks, to take a more in depth look at the Kallima wing pattern paper.
But before I do, in the interests of combating the creationist duplicity I've observed all too frequently in my travels, it's apposite to cover some ground, with respect to the structure of a scientific paper. Authors of scientific papers follow a well-defined set or rules when compiling papers for submission, dividing the contents of the paper into specific sections, and in the case of the first section, the abstract, this frequently exhibits a particular form of exposition of the contents. That form consists of the following steps:
 Present a brief summary of the state of knowledge before the submission of the new research in the paper, including the outstanding question that the newly submitted research is intended to answer;
 Summarise the experimental findings the authors have covered in more details in the later sections of the paper, and why those findings provide an answer to the outstanding question in step  above;
 Present the conclusion derived from the findings in step  above (the reasons why that conclusion is a robust conclusion to draw, appearing at the end of the paper in the Discussion section).
All too often, one of the more mendacious approaches taken by creationists to the emergence of embarrassing scientific papers, is to quote mine them for comments contained therein, that are pertinent to the state of knowledge before submission of the new research, whilst ignoring completely the rest of the paper, in which that new research is expounded, and the answers to the outstanding questions presented. Another favourite creationist trick is to subject to rampant apologetic abuse, the language used in the paper, which is frequently couched using what I term "the scientific subjunctive". This form of language presents the new findings, in the honestly tentative manner that scientists always present their findings to other scientists, with frequent appearance of subjunctive forms such as "may" or "might" in the text. This language is adopted, precisely because the research is new, and is being submitted to other scientists for peer review, with the intent that once the paper is accepted for publication, that research becomes a new addition to the prior art that can be cited by future authors. In short, the language is chosen to make explicit the basic approach, "here is our new data and experimental results, here are the conclusions we draw therefrom, and the reasons we consider said conclusions to be robust", the idea being that it is left to other reviewers to decide whether they agree with this, said agreement being signalled by publication of the paper.
The moment the paper is published, however, it is then understood that appropriate, knowledgeable reviewers have agreed with the authors, that the results do indeed lead to the stated conclusions, and that the work in question is a proper addition to the grand scientific lexicon. So let's kill off right from the start, the duplicitous apologetic misuse of scientific papers by creationist pedlars of worthless apologetics, before moving on to the exposition of the actual paper.
So, time for the paper proper. The citation is as follows:
Gradual And Contingent Evolutionary Emergence Of Leaf Mimicry In Butterfly Wing Patterns by Takao R. Suzuki, Shuichiro Tomita and Hideki Sezutsu, BMC Evolutionary Biology, 14:229-241 (25th November 2014) [Full paper downloadable from here]
Let's begin with that abstract I've described above (additional emphases mine):
Note the format I described above - , Here's a currently unanswered question;  Here's the work we did to answer that question;  Here's our answer.
So, we move on to the actual meat of the paper ...
So, immediately, after expounding a little on the history of the topic, the authors move to the matter of how to answer the question, citing prior research (the numbers in square brackets tally with a list of papers at the end) establishing that there exists what is known as the "Nymphalid Ground Plan", a collection of spatially arranged pattern elements on the wings of Lepidoptera in this Family (other ground plans for other Families also exist), and that this ground plan has been found to be present in every species thus far studied. As a consequence, the presence of this ground plan would allow for the arrangement of pattern elements between different species to be analysed, and the specific modification of that ground plan for each species mapped. Work could then, of course, be pursued detecting the genetic basis of that gound plan (citation  in the papers list is for a paper covering some of the work in this field), and the relevant genetic differences in each lineage could then be elucidated. This would provide a powerful insight into the manner in which these wing patterns are generated.
Furthermore, since all of these butterflies share a common ancestor, the genetic data would allow a phylogeny to be constructed, which is, in effect, an inheritance tree mapping the steps from common ancestor to present day lineages. Once that tree is constructed, scientists can then work backwards, determine the likely wing pattern possessed by the original common ancestor, and determine how each modern, extant lineage acquired its particular pattern in a stepwise fashion.
I'll pause for a moment to address the "imperfect mimic" question alluded to above, which has actually been answered quite neatly by another paper in my collection, in which it was determined through experiment that even a poor quality mimic will have sufficient additional advantage to be selectable, to the point where the new mimetic feature becomes fixed in the population. This can then, of course, be built upon, by the emergence of new features improving the degree of mimicry. This point being addressed, of course, in the interests of preventing any anticipated quote mining.
So, let's see how this was done, shall we?
So, the steps consist of:
 Map the pattern element arrangements in each species in the phylogeny;
 Use these to develop a phylogenetic tree, which will have the common ancestor at its base, including the likely pattern arrangement of the common ancestor, and the patterns of intermediates leading to the modern species;
 Use that tree to determine the steps leading from the ancestral pattern to the modern day pattern.
Of course, the actual work involved to achieve this end is pretty intricate, but that's what scientists are paid to do.
So, we move on, and see how this was done ...
So, step one, pick the species to be used in the analysis, taking care to eliminate any sampling biases. The next paragraphs cover the technical details of setting up a phylogeny, and don't need to be quoted in full in order to enhance our understanding of the process, but basically, the authors selected relevant pattern elements appearing in all species in the phylogeny, and used those as the basis for constructing the tree. It's worth covering in some detail what those characters are, and for this, we have to turn to the construction of the basic Nymphalid Ground Plan (NGP), which consists of three distinct major spatial zones (there's a nice illustration in the paper of these) - namely, the basal symmetry zone (closest to the wing root), the central symmetry zone and the border/ocelli symmetry zone. A fourth, narrower region, the marginal symmetry zone, is found near the wing edges. Within the basal symmetry zone, there are two bands, the proximal and distal bands, marking the effective boundaries of that zone, and there is also a proximal and distal band marking the boundaries of the other two symmetry zones. Each wing also has a discal cell, with associated mobile elements, known collectively as the baso-discal complex, which manifests as markings within the discal cell of the wing. The eye spots in the border/ocelli symmetry zone are nucleation sites within which genes controlling eyespot formation are expressed. Note that 'proximal' means closest to the wing root, and 'distal' means closest to the wing edge.
So referring to the diagram in Figure 1 of the paper, the character traits found in Kallima are:
 Parallel alignment of discal spot and border symmetry zone;
 Attachment of discal spot to central symmetry zone proximal band;
 Central symmetry zone distal band a single, unbroken straight line;
 Bending of border symmetry zone proximal band to distal side;
 Upper side of border symmetry zone proximal band straight;
 Eyespots in forewing border symmetry zone vestigial;
 Fragmentation of central symmetry zone proximal band in hindwing;
 Vestigial basal symmetry zone in hindwing;
 Vestigial discal spot in hindwing;
 Central symmetry zone distal band straight;
 Eyespots in hindwing border symmetry zone vestigial;
Now, it's worth noting at this point, that there are numerouswhich have been demonstrated via appropriate laboratory experiments to be governed by a range of genes, including invected, engrailed, distal-less, aristaless2, wingless, wntA and optix, among several others. Many of these genes are involved in spatial pattern arrangement, whilst optix is involved in colour-filling of spatial elements. I've already cited the papers containing these results in past posts, so further citation is superfluous at this juncture. Different lineages possess modifications of the genes in question, facilitating shifting of elements and changes of colour used to fill those elements. For example, wntA and wingless are expressed in the baso-discal complex and the marginal symmetry zone, with wntA further expressed in the central symmetry zone, these being determined by experimental gene knockout of the genes in question in target species, resulting in observable changes in the patterns emerging in the affected zones. Likewise, optix knockout experiments result in colour changes in the pattern elements. So, we already have a wealth of knowledge concerning the underlying molecular biology of butterfly wing patterns, and courtesy of the relevant experimental results, this is no longer in any doubt.
Moving on, a couple of details about the tree construction ...
Basically, the software used to construct the tree from the data, was able to determine additional nodes in the tree where these were not directly specified by the data, by determining the probabilities of multiple possible alternatives, and selecting the most probable ones to be members of the final tree.
Moving on, a brief word about the statistical modus operandi in action, for those familiar with the topic of Bayesian analysis ...
Now we get to the meat of the paper, namely, determining the order of changes of those 11 characters!
So, having determined the likely dependencies between the character state changes, the authors deliver their admittedly long coup de grace, as follows:
So, not only did the authors reconstruct the changes required to produce the Kallima wing pattern from an ancestral, generic NGP, but also determined the time order in which these changes occurred. I'd say this is a pretty powerful result.
And finally, the discussion:
Bingo. Task completed.
Furthermore, we have this:
So, not only did the authors determine that the leaf mimicry pattern of Kallima butterflies occur in a stepwise manner, with well-defined state transitions of pattern elements in a specific temporal order, but they also used that analysis to determine the emergence of patterns in other, non-mimetic butterflies used in the analysis.
Furthermore, seemingly in anticipation of my own caveats about treating naive views of imperfect mimicry in an injudicious manner, the authors provide this:
Ah, beautiful. Don't you agree?
The authors close their discussion with:
The authors thus conclude:
This is how it's done. Science, it works. Bitches. :D
Now of course, all that is needed to solidify this into a pretty much impregnable edifice, is tracking of the genes in the requisite species, and that work is underway as I write this. It merely remains for me to hope that my proofreading has eliminated errors before I post this three hours or work. :)
Indeed, this is an elementary concept that those of us who paid attention in biology class understand only too well. The abject failures only appear once. They end up becoming lunch for something else, and don't breed as a consequence. Of course, in the real biosphere, a good number of competent organisms end up becoming lunch for something else as well as the disasters.
Trouble is, mythology fetishists are so hung up on notions of "perfection" and other ideas that are a blind alley in biology, that they're frequently incapable of registering what their own senses are telling them.
Bloody Nora...you've edumacated me no end! Thank you...your file is bulging and so easy to read...Thank you Cali....
Wonderful experiments that prove evolution... Thanks a lot, Calilasiea!
Can you Boil it down for us calisesia w out gobs of text?
What might be noteworthy is.....
“However, the process by which leaf patterns evolved remains unclear.”
Can you address the fact that You are up against a random numbers game no matter how many experiments and observations you conduct.
When I say “ just what the katydid needed”, I am obviously referring to the fact that randomness on many counts got it what it needed, digest that for a while.
"randomness on many counts got it what it needed,"
No it didn't as there was no need, or end goal at all, evolution hasn't finished, it is a constant process, so your claim is still nonsense. Random mutations either are successful, and are passed on, or they are not. We are simply seeing billions of years of natural selection shaping all living things to perfectly match their environment.
Didn't you read any of my explanatory paragraphs between the quoted sections of the paper, which were provided specifically for that purpose?
So despite me providing not only a full exposition of the paper, but explicit warnings against quote mining, you launch into as blatant and banal a quote mine as only a creationist could. Congratulations for demonstrating that my measures in this vein were justified.
What part of the authors' conclusions at the end that I emphasised in boldface did you not read when performing your cheap and duplicitous quote mine? Or, for that matter, what part of my exposition of the modus operandi of scientific paper writing at the beginning did you also not read? The exposition where I explicitly stated, that the format consists of "here's a problem to be addressed, here's the work we did to address it, and here's our conclusions arising from that work?"
A reminder of one the bits you skipped during your quote mining:
This is as unambiguous a statement of success of the endeavour as anyone reading the paper honestly could wish for. I conclude by your pathetic response above, that you are neither interested in honest discourse, nor honest appraisal of scientific research, but instead are intent solely on propagandising for your sad little doctrine. But I didn't provide this exposition for your benefit, because I've had over a decade's worth of experience elsewhere of creationist mendacity, and therefore had no expectation that you would respond with anything other than a manifestly duplicitous evasion of the data. Others here who have already benefited from the exposition I've provided, will no doubt subject your sleazy little pseudo-response to the contempt it manifestly deserves.
Translation: "I don't care how much data destroys my assertions, I'm going to keep peddling them", which is all you're offering here.
What part of "the experiments in question demonstrate that this happened" do you not understand?
Though once again, the fact that scientists and mathematicians have placed what you snidely dismiss as "a random numbers game" on a rigorous footing, is another of those inconvenient facts you'll squirm to avoid at all costs, because that diligent effort on their part destroys your infantile posturings.
Furthermore, when mechanisms exist allowing randomly emerging new features to persist, which is clearly and demonstrably the case from thousands of examples in the biosphere, your apologetics simply look even more underhand and dishonest than before. But I don't expect creationists to be anything else, not least because they have to keep lying to themselves in order to continue propping up their worthless, evidence-free, assertion-laden doctrine. Quite simply, all you have to offer here is fatuous stonewalling coupled to blatant fabrication, and you're fooling no one with your egregious abuse of proper discourse.
Heard of the Ninth Commandment, have you? I suggest you apply it sometime, given that you're such an enthusiast for the mythology containing it.
"boom" 10,000 agrees to you sir...
“No end goal at all”
But to end up w a breathtaking replica of a leaf which benefits the insect is surely beating the odds at life’s numbers game. And you evos seem to be way ahead of the odds. Something is quite suspicious here, I’m thinking some intelligent Design at play.
Whenever you say “evolve”, you are at the mercy of chance luck, no 2 ways about it
JNV3, you wrote, “But to end up w a breathtaking replica of a leaf which benefits the insect is surely beating the odds at life’s numbers game.”
Just what are the odds you assert are being beaten?