Coded Logic

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Posts by Coded Logic

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  205

  Mathematically Measuring Evolution.

  by towerwatchman in

  1. watchtower
  2. beliefs

  mathematically measuring evolution.. when judging relationships in terms of morphological characteristics we will always be bound by the subjective.

  morphologically one cannot exactly measure the distance between two organisms strictly in mathematical terms.

  using the standard method of taxonomy we cannot quantify the difference between a horse and a mouse, or know which is closer mouse to cat, or mouse to fish.

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  Coded Logic

  • Stop hiding in the obscure, gray, subjective world of comparative anatomy, and step in to the objective world of mathematics and genetics.
    -TWM

    I think there's something deeply dishonest about you making this claim. Multiple people on this forum - myself included - have attempted to engage you on the mathematics and genetics. I even went so far as to post the actual calculations used and the different methodologies.

    Instead of addressing any of the points raised, you instead copy and pasted this multiple times:

    Let’s talk about chimp to man. Evolutionist say that the difference between man and chimp is 1.5 %. Does not seem much. What we need to find out is how much is much. When we hear that there is a 1 ½ % difference between man and chimp it seems not to be much. But we must take into account what 1 ½% exactly means. If there are three billion base pairs in a human 1 ½% calculates to 45 million base pairs or 15 million codons. It is estimated that it would take 10X10^21 mutations to get five condons to mutate in the right order. One and half percent does not look like much but when analyzed, it becomes overwhelming evidence against man ever evolving from a chimp.

    
    
    Let me be as clear as I possibly can
    
  • . . .
    THIS:
    
    
  • . . .
    Is NOT this:
    
    It'd be like if I explained the complexities of a Saturn V Rocket and someone said, "Well I don't think we ever went to the moon because a pogo stick could never jump that high."
    
    Likewise, after I went into the science and mathematics of Mitochondrial DNA, the X Chromosome, Allele Frequencies, and Endogenous Retro Virus' - for you to bring up how much DNA we share with chimps, and then turn around and object to what I said on those grounds - is absolutely bone headed and doesn't come even close to addressing to the very real science I raised.
    
    Once again, let me be clear: Pogo sticks are NOT what we used to get to the moon. And overly simplistic shared DNA stats are NOT how we use genetics to demonstrate common ancestry.
    
    If you want to talk about the mathematics and genetics than let's talk about the mathematics and genetics. But in order for us to do that you're going to have to stop hiding behind this cheap strawman that you've concocted.
    
    Nobody is going to be able to have a meaningful conversation if you don't engage with them honestly.
    
    
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  205

  Mathematically Measuring Evolution.

  by towerwatchman in

  1. watchtower
  2. beliefs

  mathematically measuring evolution.. when judging relationships in terms of morphological characteristics we will always be bound by the subjective.

  morphologically one cannot exactly measure the distance between two organisms strictly in mathematical terms.

  using the standard method of taxonomy we cannot quantify the difference between a horse and a mouse, or know which is closer mouse to cat, or mouse to fish.

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  Coded Logic

  What you have is a fish with five unique bones . . .
  - TWM

  Except, of course, that their bones aren't "unique" are they? Did you notice the hand bones in Ticktallik are the same bones we see in the hands of every reptile, bird and mammal alive today?

  
  

  
  

  
  

  
  

  . . .
  But it doesn't stop there does it? Prior to the Tiktaalik, we don't see ANY land animals do we? And as we move up through the geological column we see these "unique fish" looking more and more reptilian.

  
  

  . . . and someone's opinion based on comparative anatomy that it is a transitional species.

  Except, of course, that it's not based on "someONEs" opinion is it? Rather, it's based upon evidence, research, peer review, and scientific consensus isn't it?

  
  http://courses.washington.edu/bio354/Paper%203.pdf

  http://www.nature.com/news/2006/060405/full/news060403-7.html

  http://www.academia.edu/407901/Tetrapod_Trackways_From_the_Early_Middle_Devonian_Period_of_Poland

  Comparative anatomy will always be gray and ambiguous.

  Except, or course, that it's neither of those things is it? Instead, far from being "ambiguous" we know that Comparative Anatomy is a scientific field of study - subject to all the rigors and scrutiny imposed by the process' or verification and falsification.

  And isn't it also true that Comparative Anatomy is based upon work done by scientists who are experts in their fields and who have spent decades researching their respective findings? Scientists who understand the difference between Homologuous, Analogous, and Homoplastic Structures - just to start with the basics. But, of course, you wouldn't know anything about that would you?

  And isn't it also true that the findings of Comparative Anatomy are backed up by modern day DNA sequencing? Please tell me, how a whole scientific enterprise - one that's been demonstrated to be a reliable method for making determinations about species - can be called "gray" or "ambiguous"?

  Just a thought, but before you go dismissing the work of an entire field of study - perhaps you should learn something about it first

  We all know you don't have a bone to pick with Comparative Anatomy because you have well researched and informed opinion. Rather, the only reason you're objecting is because it conflicts with you preconceived notions about creationism.
  

  We DON'T see you running around saying "particle physics is just someones opinion". Or, "chemistry will always be gray and nebulous" even though they're based upon the exact same types of inferences and deductions as Comparative Anatomy.

  What you have is hundreds of fossils that demonstrate a common designer.

  
  

  Alright, I'll bite. How do these hundreds of fossils demonstrate a common designer? And what empirically reliable method did you use to make this determination?
  
  

  
  
• 
  205

  Mathematically Measuring Evolution.

  by towerwatchman in

  1. watchtower
  2. beliefs

  mathematically measuring evolution.. when judging relationships in terms of morphological characteristics we will always be bound by the subjective.

  morphologically one cannot exactly measure the distance between two organisms strictly in mathematical terms.

  using the standard method of taxonomy we cannot quantify the difference between a horse and a mouse, or know which is closer mouse to cat, or mouse to fish.

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  Coded Logic

  Just out of curiosity, do you think something has to be EXACTLY halfway between two species to be considered "transitional"? Re-reading your last reply I almost get the feeling you think the Archeoptryx can't be considered transitional because it's too avian?

  I hope this isn't your position because - if it is - it's frankly a rather silly one. It'd be like saying your cousin can't be a retaliative of yours because he's not enough like your great-grandfather and is too much like your mother.

  Likewise, transitional species aren't the halfway point of any two groups. Rather, they're a species that are somewhere in the link between two other species.
• 
  205

  Mathematically Measuring Evolution.

  by towerwatchman in

  1. watchtower
  2. beliefs

  mathematically measuring evolution.. when judging relationships in terms of morphological characteristics we will always be bound by the subjective.

  morphologically one cannot exactly measure the distance between two organisms strictly in mathematical terms.

  using the standard method of taxonomy we cannot quantify the difference between a horse and a mouse, or know which is closer mouse to cat, or mouse to fish.

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  Coded Logic

  Well, I'm happy to see that we've once again made some mild progress. We've gone all the way from Archeopteryx being "just a bird" to a "bird with unique features" and now you've reached the threshold of calling it "truly unique".

  Except of course that Archeopteryx isn't "truly unique" is it? In fact, when we look at the Jurassic and Triassic period, there are many other Theropods with with both feathers and reptilian features. There are a huge number of these dinosaurs (or as you call them "birds") such as:

  1. Avimimus portentosus
  2. Sinosauropteryx prima
  3. Protarchaeopteryx robusta
  4. Caudipteryx zoui
  5. Rahonavis ostromi
  6. Shuvuuia deserti
  7. Beipiaosaurus inexpectus
  8. Sinornithosaurus millenii
  9. Caudipteryx dongi
  10. Caudipteryx
  11. Microraptor zhaoianus
  12. Nomingia gobiensis
  13. Psittacosaurus
  14. Scansoriopteryx heilmanni
  15. Yixianosaurus longimanus
  16. Dilong paradoxus
  17. Pedopenna daohugouensis
  18. Jinfengopteryx elegans
  19. Juravenator starki
  20. Sinocalliopteryx gigas
  21. Velociraptor mongoliensis
  22. Epidexipteryx hui
  23. Similicaudipteryx yixianensis
  24. Anchiornis huxleyi
  25. Tianyulong confuciusi
  26. Concavenator corcovatus
  27. Xiaotingia zhengi
  28. Yutyrannus huali
  29. Sciurumimus albersdoerferi
  30. Ornithomimus edmontonicus
  31. Ningyuansaurus wangi
  32. Eosinopteryx brevipenna
  33. Jianchangosaurus yixianensis
  34. Aurornis xui
  35. Changyuraptor yangi
  36. Kulindadromeus zabaikalicus
  37. Citipati osmolskae
  38. Conchoraptor gracilis
  39. Deinocheirus mirificus
  40. Yi qi
  41. Zhenyuanlong suni
  42. Dakotaraptor steini
  43. Apatoraptor pennatus

  . . .

  It's pretty awesome. When we look back to the Triassic and Jurassic periods we don't see ANY modern birds. And all the animals we see that have feathers also have extensive reptilian features. Why is that?

  It's simple. Because some of the dinosaurs were the precursors to modern day birds.

  You correctly pointed out that some of these dinosaurs we're quite likely capable of short flight (like the micro-raptor). But what you left out was that most of these feathered dinosaurs couldn't fly at all. Their arms were still arms. Not wings.

  Some of these animals - like the Sinosauropteryx - were thought to be ordinary dinosaurs . . . until we found imprints of their feathers. That is to say, outside of their feathers, there is nothing avian about them. Would you call Sinosauropteryx a "bird"? And if we call a Sinosauropteryx a bird - than what about other types of Compsognathidae that don't have feathers but are closely related? Are they all "birds" too? And if they are all birds too, should we also call all Coelurosauria "birds" as well? Does this mean that the mighty T-rex is a "bird"?

  
  

  There's a lot more here than you realize. And the Archeopteryx is by no means a one off. It's what birds used to look like - when they were still dinosaurs.

  On a separate note, I'd also like to point out that there is something between scales and feathers. They're called protofeathers. Check it out:

  http://people.eku.edu/ritchisong/feather_evolution.htm
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  11

  GoBo hints we want all to dress American I

  by oppostate in

  1. social
  2. humour

  in this wt literature illustration from a german kingdom hall, one can see that the two nonwestern jw's on the right are featured as needing to improve on their choice of clothing and become more american like the gobo wishes them all to be.. .. .

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  Coded Logic

  The brothers on the left are wearing baggy clothes (very worldly of them), aren't visiting jw.org on their phones, and are making homoerotic eye contact with each other. They clearly need to be counseled.
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  205

  Mathematically Measuring Evolution.

  by towerwatchman in

  1. watchtower
  2. beliefs

  mathematically measuring evolution.. when judging relationships in terms of morphological characteristics we will always be bound by the subjective.

  morphologically one cannot exactly measure the distance between two organisms strictly in mathematical terms.

  using the standard method of taxonomy we cannot quantify the difference between a horse and a mouse, or know which is closer mouse to cat, or mouse to fish.

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  2. 
  3. 
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  Coded Logic

  3.) Alelle Frequencies:

  We can start off with the Hardy-Weinberg equation which is expressed as follows

  p2 + 2pq + q2 = 1

  where p is the frequency of the "A" allele and q is the frequency of the "a" allele in the population. In the equation, p2 represents the frequency of the homozygous genotype AA, q2 represents the frequency of the homozygous genotype aa, and 2pq represents the frequency of the heterozygous genotype Aa. In addition, the sum of the allele frequencies for all the alleles at the locus must be 1, so p + q = 1.

  
  

  Or, if we want to look more broadly at the genotype - we'd need to use a multinomial distribution in which genotype frequencies are f(AA) = p2 for the AA homozygotes, f(aa) = q2 for the aa homozygotes, and f(Aa) = 2pq for the heterozygotes.

  
  

  
  

  
  

  
  
• 
  205

  Mathematically Measuring Evolution.

  by towerwatchman in

  1. watchtower
  2. beliefs

  mathematically measuring evolution.. when judging relationships in terms of morphological characteristics we will always be bound by the subjective.

  morphologically one cannot exactly measure the distance between two organisms strictly in mathematical terms.

  using the standard method of taxonomy we cannot quantify the difference between a horse and a mouse, or know which is closer mouse to cat, or mouse to fish.

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  Coded Logic

  2.) X Chromosome

  This one's a little easier to figure out as it's practically a Fibonacci number. Here are the numbers we need:
  

  
  

  Though I do prefer this chart as it's a little more intuitive:
  
  
  
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  205

  Mathematically Measuring Evolution.

  by towerwatchman in

  1. watchtower
  2. beliefs

  mathematically measuring evolution.. when judging relationships in terms of morphological characteristics we will always be bound by the subjective.

  morphologically one cannot exactly measure the distance between two organisms strictly in mathematical terms.

  using the standard method of taxonomy we cannot quantify the difference between a horse and a mouse, or know which is closer mouse to cat, or mouse to fish.

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  Coded Logic

  If we really do want to measure evolution we're going to have to be willing to do the math. Not sure how deep you want to get into this but the information is readily available for anyone who wants to take a stab at it.
  

  Also, I agree with Caedes. It would be nice if you could provide the source for your OP and the mathematics you used to reach your conclusion.

  Of the four methodologies I provided to look at our DNA here are some of the calculations we can use -

  1.) Mitochondrial DNA:
  

  

  The variable RW above is the average fraction of wild-type nucleoid among mitochondria (i.e. the average of (1−RM,imito)) in a cell. The sigmoidal function is motivated by the activity data of cytochrome c oxidase (COX) as a function of the relative proportion of wild-type and mutant mtDNA in cybrid cells (see Fig. 1B) [38]. COX is an enzyme complex involved in the mitochondrial ATP production and its activity is used as an indicator of mitochondrial respiration function. Based on the equation above, the maximum amplification of mtDNA replication by retrograde signaling (at RW = 0) is rmax +1, which has been reported to be ∼16 times the basal rate [39]. A linear function can also be used in place of the sigmoidal function above, without changing the general trend and conclusions from the model simulations

  
  

  (A) During a mitochondrial fusion, the nucleoid information (W and M) of the precursor mitochondria is retained and a fission site is created (bold line). During fission of a previously fused mitochondrion, a fission site is randomly chosen from the possible sites in the mitochondrion selected for fission. The redistribution of nucleoid contents between the two daughter mitochondria is determined randomly according to a Binomial distribution, while the particular nucleoids to be transferred are randomly taken from a Hypergeometric distribution. During fission of a primary mitochondrion, i.e. mitochondrion without any fission site, nucleoids are randomly distributed between two daughter mitochondria. (B) Steady state distribution of mitochondrial size as a function of mitochondrial size. In the figure inset, the fission propensity is shown as a function of mitochondrial size (number of nucleoids). (C) Mitochondrial fusion-fission and nucleoids mixing rate. Mitochondrial heterogeneity in each cell is represented by the mean coefficient of variation (COV) of RMmito. The mean COV of RMmito is scaled such that the steady state value is −100%. In this case, the mixing time τ is defined as the time for the scaled COV of RMmito to reach −63.2%. A faster decrease in the mean COV of RMmitoindicates a faster mixing and hence is indicated by a smaller mixing time constant τ.
  
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  205

  Mathematically Measuring Evolution.

  by towerwatchman in

  1. watchtower
  2. beliefs

  mathematically measuring evolution.. when judging relationships in terms of morphological characteristics we will always be bound by the subjective.

  morphologically one cannot exactly measure the distance between two organisms strictly in mathematical terms.

  using the standard method of taxonomy we cannot quantify the difference between a horse and a mouse, or know which is closer mouse to cat, or mouse to fish.

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  2. 
  3. 
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  Coded Logic

  Hahaha, well I suppose I should be happy that you've changed your position from Archeopteryx is "just a bird" all the way to Archeopteryx is "just a bird with unique features". I guess that's progress.

  ;)

  But, if we're being honest, it's NOT just a bird with unique features is it? It's a "bird" with features that are inherently reptilian. It's a "bird" with the exact sort of features we would expect to see during a speciation event in which "birds" were much more like their dinosaur precursors.

  Not only that, if you'll recall, you were the one to bring up morphological and anatomical differences. I'm not sure it's really fair to cry foul (or perhaps, in this case, fowl) now that it's "too subjective" a topic since you've decided you don't like where the evidence is leading.

  But all that's neither here nor there. To you're broader point, we have a multitude of mechanism for looking at and measuring the difference in species. We can do this in several different ways:

  1.) Mitochondrial DNA

  2.) X Chromosomes

  3.) Endogenous Retrovirus'

  4.) Allele Frequencies

  These are each independent methods of studying various aspects our DNA to determine hierarchy. For example, evolution predicts that our closest cousins are chimpanzees', followed by guerrillas and then orangutans. And when we look at our mitochondrial DNA (this is what's used in paternity and ancestry tests) we observe the exact same thing.

  The same is true when we look at the family lines along the x-chromosome. We find that human's closest cousins are chimpanzees followed by guerrillas and then orangutans.

  Next, we can do something very different. We can see what endogenous retrovirus' (ERVs) we share with other animals. According to evolution, we should expect that any ERVs we share with orangutans we'd also share with guerrillas and chimpanzees since orangutans are our most distant ape cousins. And, conversely, we'd expect that there would be some ERVs we'd share with chimpanzees and guerrillas that we don't share with orangutans. Guess what? This is exactly what we observe!

  Lastly, we can look at allele frequencies (or, more broadly, genotype frequencies). And the species with which humans have the lowest number of genetic variants is . . . you guessed it, chimpanzees! Wow, what a stunning surprise. Want to wager which species might be next closest? Or next closest after that? Why guerrillas and orangutans of course!

  So there we have it, four independent methods of studying DNA that all converge on the exact same hierarchy. But we don't have to stop there. There's a host of other methods we can use too!
  

  5.) Homologous Structures

  6.) Vestiges

  7.) Atavisms

  8.) Phylogenetic Heterogeneity

  9.) Allopatric Speciation

  . . .

  And want to guess the hierarchy at which all these methods also arrive?

  This is an important point. There's not just lot's of evidence for evolution. There's lot's of methodologies that all converge on the same answer. In science, having two independent methods reaching a similar conclusion is generally considered rock solid. In biology, evolution doesn't just have two. There at least nine that I know of (and I'd not be surprised if there are even more).

  In closing, I'd like to mention I don't think there's anything wrong with your skepticism (a demand for evidence). So long as you stay true to the flip side of that coin as well - keeping an open mind (aka - following that evidence where it leads).
• 
  205

  Mathematically Measuring Evolution.

  by towerwatchman in

  1. watchtower
  2. beliefs

  mathematically measuring evolution.. when judging relationships in terms of morphological characteristics we will always be bound by the subjective.

  morphologically one cannot exactly measure the distance between two organisms strictly in mathematical terms.

  using the standard method of taxonomy we cannot quantify the difference between a horse and a mouse, or know which is closer mouse to cat, or mouse to fish.

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  2. 
  3. 
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  Coded Logic

  But what is unique to evolution is the amount of imagination that is used. All you have here is a bird.

  -Towerwatchman

  No imagination necessary my friend. There are multiple lines of evidence showing that Archeopteryx is more than just a bird:

  1.) All modern birds have beaks or bills. The Archeopteryx, however, does not have a beak. Instead, it has a jaw.

  2.) The spinal cord in modern birds attaches underneath the skull. In Archeopteryx, the spinal cord attaches to the back of the skull (like all other reptiles).

  3.) The thoracic vertebrae in modern birds is always fused. In Archeopteryx, the thoracic vertebrae are free.

  4.) Modern birds have a saddle shaped cervical vertebrae. Archeopteryx has a cervical vertebrae with conclave vertical facets (much like Tarbosaurus).

  5.) Birds have short articulating ribs. The Archeopteryx, however, has long ribs that do not articulate.
  

  6.) Birds do not have a gastralium. Archeopteryx, like all reptiles, does.

  7.) Birds metacarpals (hand bones) are always fused. But the metacarpals of Archeopteryx, like all reptiles, are free and flexible.

  8.) Birds have 11 to 23 vertebrae in the sacrum (the vertebrae that run through the pelvis). The Archeopteryx has only six bones in it's Sacrum (the same number as in reptiles).

  9.) Birds have an elongated pubis that angles backward. The pubic shafts of Archeopteryx is short and not angled backward.

  10.) Birds have a short tail with the vertebrae at the end fused into a pgostyle. The Archeopteryx has a long boney tail with many free vertebrae up to the tip.

  There are many other differences too that put the Archeopteryx is more than just a bird.