The Coccyx

[pshun2404]

Psycho...this has to do with specific genes and their functions (a few of which we know)...

Now when I hear about development and diversification of a species (phylogeny), I do not have one bit of doubt as to that process. I can see natural selection, genetic drift, allele reinforcement, and so n ALL being in effect. Except, the only evidence that I can actually SEE is the production of variation within a particular species. I can SEE the production of various sub-species (like in Darwin’s finches, E-Coli, Picea Abies, and more), but what I cannot see is the production of entirely different organisms (like amphibians becoming reptiles and so on) as represented in a typical phylogeny.

I realize that, as I had been taught, the explanation is that “shared genes” or similarities in the genomes shows “relationship”, but phylogenesis? I no longer believe that is the only explanation of what we have here.

They define this relationship as proof of lineage, but all it really is, is proof of similarity (which could be present for any number of reasons). Organisms in their specific groups all share anatomical and physiological similarity. I realize now that “relationship” does not automatically imply progeny.

Now yes, if we design algorithms (such as in computational phylogenetic programs) where WE INPUT the parameters and guidelines we get some semblance of the result we expected (GIGO) but people with this expectation and belief made the program design (that’s like stacking the deck). Of course they are not going to get results that contradict what they planned to discover. The question, “Does Computational Phylogenetics indicate lineage?”, the answer will always be yes because that expectation is built in and being looked for.

These analyses do not tell us that many of the “selected sections” being sequenced, in fact are often found in different places in the respectful gnomes, AND often have very different functions. For some examples when the data is given void the explanation, according to Gagneux and Varki in, ‘Genetic differences between humans and great apes.’ Mol Phylogenet Evol 18:2-13 (2001), we can see differences in:

type and number of repetitive genomic DNA sequences,

a number of transposable elements,

the abundance and distribution of endogenous retroviruses,

the presence and extent of allelic polymorphisms,

specific gene inactivation events,

gene sequencing differences,

gene duplications,

single nucleotide polymorphisms,

gene expression differences,

messenger RNA splicing variations


And more

 

[pshun2404]

The prior post as well as this all speaks to the notion that we have genes for growing tails and having gills and how I know you do not know this you suppose it because you accept the explanation as true.

As posted elsewhere, just look at this alleged “same gene” across species...an ALLEGED shared gene...

Human Gene HDLBP (uc002wba.1) a 110-kD protein that specifically binds HDL molecules, which functions in the removal of cellular cholesteral...it is a section 87,092 base pairs long

Rat Gene Hdlbp (NM_172039) which is only 68, 238 base pairs long performs a similar function but apparently not identically.

The allegedly the “SAME GENE” in Yeast, S. cerevisiae Gene SCP160 (YJL080C) functions differently and is primary to cell division, and only has 3,669 base pairs.

And finally, the alleged “SAME GENE” in D. Melongaster, Gene Dp1 (CG5170-RB). Having 9119 base pairs (3 times that of Yeast) seems to do nothing!

Now as far as the hypothesis based explanation appears, this actually contradicts it not supports it. While they appear to be shared among many organisms (some older some more recent), the actual data produced shows us they are actually nothing alike...they are different in size, and different in function...yet billed as “commonly shared” in the rhetoric.

Then there are things noted by others, such that the same genes in some species producing different results as seen above being complimented (or complicated depending on the presupposition) by the same result in different species involving and requiring totally different genes.

Since phylogenesis in terms of transmutation of one organism onto another apparently happens by speciation of great lengths of time, then these accumulated changes (such as by mutations) are accepted as having the power to entirely transform (albeit very slowly) entire anatomical and physiological aspects of the original (allegedly parent) organisms. Only though surely organisms accumulate mutation, and along with other factors, these lead to speciation, but all examples from nature we can and ever have observed (including all those tests accomplished in labs), only produce variation of the SAME ORGANISM. In other words, we can prove this causes variety, but not a transformation of progeny such as a phylogenetic tree presents.

 

[pshun2404]

Hey pshun - just wanted to remind you about these parts of the post that you deigned not to respond to before, just by accident I am sure:

Thanks!

I'm sorry, what was "deigned...to respond to"? I saw that post as typical criticism from denial and thus no reason to respond.

 

[pshun2404]

-_- phylogeny is derived from variability in genetics. The palmaris longus muscle ...Phylogeny is the diversification and development of a species (such as our own). The fact that some people have the muscle in both arms, some people have it in one arm and not the other, and some people don't have it at all is an example of diversity in our species.

What did you think phylogeny meant? Although, none of this has to do with the fact that the palmaris longus muscle is vestigial. .

in old world monkeys all in some varieties have it...all in others do not...it is variable in Gibbons...present in Orangutans, variable in gorillas, chimps, and humans...so what. None of this demonstrates the palmaris longus muscle is vestigial. It is an inheritable characteristic within each species but for "vestigial" to fit, it would have to be something there that is now less or left over. Calling it that or interpreting it as that is subjective (again theory based).

 

[pshun2404]

Curious as to why the great argument analyzer did not address any of this...

or this:

"The great argument analyzer"! Wow! That's a new one. I do not agree that the evidence you presented demonstrates vestigiality. It does not show or demonstrate the coccyx was more and is now less. YES it is longer and/or part of additional structure in OTHER organisms but that only implies vestigial if we came FROM them. You believe we do, thus you believe it proves it.

 

[pshun2404]

LOL!

Then please be the first to produce empirical evidence for your Faith. Start a new thread - heck, I will start it for you.

No

No

And fine go for it...

 

[xianghua]

On the genetic level, the presence of genes in our DNA which, if active, would promote the formation of a tail.

any reference?

There is no reason for us to have genes for the formation of a tail or gills if we didn't have ancestors with those traits.

humans also have genes for feathers development. does its means that humans evolved from birds?:

http://phenomena.nationalgeographic.com/2014/11/20/your-inner-feather/

 

[xianghua]

i suspect you did not read the article.

"It may seem strange to consider the fact that you, as a mammal, have all the known genes required to pattern a feather, and yet you do not look like Big Bird. The reason for this discrepancy is that genes can do different jobs."

Mammals and birds did share a common ancestor. A long time ago.

its actually was sarah argument:

"There is no reason for us to have genes for the formation of a tail or gills if we didn't have ancestors with those traits."

so by the same logic we can say that the fact that human have genes for feathers development prove that human ancestor had feathers.

 

[pshun2404]

"Do chimp embryos have tails? Do chimps?"

No and NO

 

[pshun2404]

Yes that was worded very poorly. The point, though misstated on my part, was only in context of a greater list of examples where (and not all is questionable) comparative genomics is not a perfect science. There are many examples however of how surrounding codons do effect codons and sets of codons that their function is dependent on, and these vary between species. I am surprised you have not come across any but granted it is still young as developing thought.

Some of these instances enhance the purpose of an expression , sometimes they hinder functions (in certain plants), but generally we are now seeing as many as three codons before and after a given codon as effecting their purpose and function. These can and do encourage strong or weak expression in the relative genes, and so on. Now I care not to go off into this as a diversion from the OP but here are some articles you can read (if interested) and perhaps you will reach a different conclusion.

Case for the genetic code as a triplet of triplets

Sequence Architecture Downstream of the Initiator Codon Enhances Gene Expression and Protein Stability in Plants

Constraints on codon context in Escherichia coli genes their possible role in modulating the efficiency of translation - ScienceDirect

http://www.pnas.org/content/88/21/9789.short

The selection-mutation-drift theory of synonymous codon usage. | Genetics


“Fish embryos do not get oxygen from its mother. They do not develop gills until well into their development.”

Glad I never said that!

Perhaps you can provide a quote in which an evolutionist has claimed that a human embryo has gills to obtain oxygen.

None! Psycho said human embryos have gills (and by the way she said not to bring up the liar or his intentionally doctored inaccurate drawings)

“the term "gill slits" described their appearance, not their function.”

I 100% agree...humans never had gills, or slits that would have become gills if these alleged “gill” genes were not repressed...never happened. They do have fatty folds that can appear to look like gill slits to someone convinced of the notion that ontology recapitulates phylogeny (which from her comments I assume Psycho believes)

“Who said that the pharyngeal apparatus formed arms?”

No one!

“vertebrate embryos ALL have a stage in which they possess a pharyngeal (branchial) apparatus (they all also start with identical aortic arch patterns). In fish, the p.a. develops into gills. In mammals it goes on to form structures i the face and neck. “

I agree, and this is a perfect example of what I was speaking about, thank you, AND it shows her assumption was not correct. Same genetic source, totally different function and purpose in different organisms. Bingo!

 

[xianghua]

Look almost identical.

One has a karyotype of n=6, the other n-46

Hmmmmm.... Guess they must be different "kinds"? Tell us all about their genetics.

can they interbreed? (even by an insemination).

 

[pshun2404]

Where did you paraphrase all that from? Wells?

THE TESTED METHODOLOGY:

Science 25 October 1991:
Vol. 254. no. 5031, pp. 554 - 558

Gene trees and the origins of inbred strains of mice

WR Atchley and WM Fitch

Extensive data on genetic divergence among 24 inbred strains of mice provide an opportunity to examine the concordance of gene trees and species trees, especially whether structured subsamples of loci give congruent estimates of phylogenetic relationships. Phylogenetic analyses of 144 separate loci reproduce almost exactly the known genealogical relationships among these 24 strains. Partitioning these loci into structured subsets representing loci coding for proteins, the immune system and endogenous viruses give incongruent phylogenetic results. The gene tree based on protein loci provides an accurate picture of the genealogical relationships among strains; however, gene trees based upon immune and viral data show significant deviations from known genealogical affinities.

======================

Science, Vol 255, Issue 5044, 589-592

Experimental phylogenetics: generation of a known phylogeny

DM Hillis, JJ Bull, ME White, MR Badgett, and IJ Molineux
Department of Zoology, University of Texas, Austin 78712.

Although methods of phylogenetic estimation are used routinely in comparative biology, direct tests of these methods are hampered by the lack of known phylogenies. Here a system based on serial propagation of bacteriophage T7 in the presence of a mutagen was used to create the first completely known phylogeny. Restriction-site maps of the terminal lineages were used to infer the evolutionary history of the experimental lines for comparison to the known history and actual ancestors. The five methods used to reconstruct branching pattern all predicted the correct topology but varied in their predictions of branch lengths; one method also predicts ancestral restriction maps and was found to be greater than 98 percent accurate.

==================================

Science, Vol 264, Issue 5159, 671-677

Application and accuracy of molecular phylogenies

DM Hillis, JP Huelsenbeck, and CW Cunningham
Department of Zoology, University of Texas, Austin 78712.

Molecular investigations of evolutionary history are being used to study subjects as diverse as the epidemiology of acquired immune deficiency syndrome and the origin of life. These studies depend on accurate estimates of phylogeny. The performance of methods of phylogenetic analysis can be assessed by numerical simulation studies and by the experimental evolution of organisms in controlled laboratory situations. Both kinds of assessment indicate that existing methods are effective at estimating phylogenies over a wide range of evolutionary conditions, especially if information about substitution bias is used to provide differential weightings for character transformations.



APPLICATION OF THE TESTED METHODOLOGIES:

Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: Enlarging genus Homo

"Here we compare ~90 kb of coding DNA nucleotide sequence from 97 human genes to their sequenced chimpanzee counterparts and to available sequenced gorilla, orangutan, and Old World monkey counterparts, and, on a more limited basis, to mouse. The nonsynonymous changes (functionally important), like synonymous changes (functionally much less important), show chimpanzees and humans to be most closely related, sharing 99.4% identity at nonsynonymous sites and 98.4% at synonymous sites. "



Mitochondrial Insertions into Primate Nuclear Genomes Suggest the Use of numts as a Tool for Phylogeny

"Moreover, numts identified in gorilla Supercontigs were used to test the human–chimp–gorilla trichotomy, yielding a high level of support for the sister relationship of human and chimpanzee."



A Molecular Phylogeny of Living Primates

"Once contentiously debated, the closest human relative of chimpanzee (Pan) within subfamily Homininae (Gorilla, Pan, Homo) is now generally undisputed. The branch forming the Homo andPanlineage apart from Gorilla is relatively short (node 73, 27 steps MP, 0 indels) compared with that of thePan genus (node 72, 91 steps MP, 2 indels) and suggests rapid speciation into the 3 genera occurred early in Homininae evolution. Based on 54 gene regions, Homo-Pan genetic distance range from 6.92 to 7.90×10−3 substitutions/site (P. paniscus and P. troglodytes, respectively), which is less than previous estimates based on large scale sequencing of specific regions such as chromosome 7[50]. "



Catarrhine phylogeny: noncoding DNA evidence for a diphyletic origin of the mangabeys and for a human-chimpanzee clade.

"The Superfamily Hominoidea for apes and humans is reduced to family Hominidae within Superfamily Cercopithecoidea, with all living hominids placed in subfamily Homininae; and (4) chimpanzees and humans are members of a single genus, Homo, with common and bonobo chimpanzees placed in subgenus H. (Pan) and humans placed in subgenus H. (Homo). It may be noted that humans and chimpanzees are more than 98.3% identical in their typical nuclear noncoding DNA and probably more than 99.5% identical in the active coding nucleotide sequences of their functional nuclear genes (Goodman et al., 1989, 1990). In mammals such high genetic correspondence is commonly found between sibling species below the generic level but not between species in different genera."







Regarding GIGO - what do you think about the creationist phylogeneticists (baraminologists) that use these SAME techniques to investigate Intra-Kind relationships?

Will you dismiss them, too?

And what do you know that this guy doesn't:

The truth about evolution
I hope this doesn't turn into a rant, but it might. You have been warned.

Evolution is not a theory in crisis. It is not teetering on the verge of collapse. It has not failed as a scientific explanation. There is evidence for evolution, gobs and gobs of it. It is not just speculation or a faith choice or an assumption or a religion. It is a productive framework for lots of biological research, and it has amazing explanatory power. There is no conspiracy to hide the truth about the failure of evolution. There has really been no failure of evolution as a scientific theory. It works, and it works well.

I say these things not because I'm crazy or because I've "converted" to evolution. I say these things because they are true. I'm motivated this morning by reading yet another clueless, well-meaning person pompously declaring that evolution is a failure. People who say that are either unacquainted with the inner workings of science or unacquainted with the evidence for evolution. (Technically, they could also be deluded or lying, but that seems rather uncharitable to say. Oops.)

Creationist students, listen to me very carefully: There is evidence for evolution, and evolution is an extremely successful scientific theory. That doesn't make it ultimately true, and it doesn't mean that there could not possibly be viable alternatives. It is my own faith choice to reject evolution, because I believe the Bible reveals true information about the history of the earth that is fundamentally incompatible with evolution. I am motivated to understand God's creation from what I believe to be a biblical, creationist perspective. Evolution itself is not flawed or without evidence. Please don't be duped into thinking that somehow evolution itself is a failure. Please don't idolize your own ability to reason. Faith is enough. If God said it, that should settle it. Maybe that's not enough for your scoffing professor or your non-Christian friends, but it should be enough for you.
​

- Todd Wood, YEC, PhD (biochemistry)

Regarding GIGO - what do you think about the creationist phylogeneticists (baraminologists) that use these SAME techniques to investigate Intra-Kind relationships?

Will you dismiss them, too?

Worse! There are definite "relationships" they try to deny altogether. I see them, but more as similarity of function and purpose not lineage, again sometimes we see differences in different areas, sometimes resulting in different purpose (as you pointed out in the gill discussion). I also see the incongruence admitted here, intentionally partitioning into sub-sets (that nature does not do), as well as synonymous vs nonsynonymous features that do not fit the current accepted view of phylogeny, that gene trees based upon immune and viral data show significant deviations from known genealogical affinities, and so on (there are more, but thanks for the small book, it was very informative, and I am glad they are engaging this work and love to read more and more when I can. One day we will actually be sure about a lot of it).

But to me that's one of the best qualities of science (the method), it forces "scientists" to change the way they view things over time.

 

[pshun2404]

its actually was sarah argument:

"There is no reason for us to have genes for the formation of a tail or gills if we didn't have ancestors with those traits."

so by the same logic we can say that the fact that human have genes for feathers development prove that human ancestor had feathers.

Indeed!

 

[ViaCrucis]

Thus, the coccyx is not a vestigial tail at all because

a) as far back as we can go this feature was never a tail, never atrophied, or “degenerated” from something longer. Even in the alleged earliest human species the coccyx is short, and

Have to go back further than just the earliest humans or hominids. The loss of the tail is an ancestral trait that occurred before our ancestors diverged from the ancestors of the modern chimpanzees; tail loss occurred much further back in our evolutionary history than this as it is a universal trait among all hominoids and possibly goes back to the divergence between the ape line and the old world monkey line which would have occurred between 25 and 30 million years ago; whether the earliest apes in the fossil record had tails or not isn't something I know, I'm not sure if we can know it at all at this point since the earliest ape fossil (Rukwapithecus) isn't a complete specimen, it's a jawbone with some teeth.

-CryptoLutheran

 

[pshun2404]

Have to go back further than just the earliest humans or hominids. The loss of the tail is an ancestral trait that occurred before our ancestors diverged from the ancestors of the modern chimpanzees; tail loss occurred much further back in our evolutionary history than this as it is a universal trait among all hominoids and possibly goes back to the divergence between the ape line and the old world monkey line which would have occurred between 25 and 30 million years ago; whether the earliest apes in the fossil record had tails or not isn't something I know, I'm not sure if we can know it at all at this point since the earliest ape fossil (Rukwapithecus) isn't a complete specimen, it's a jawbone with some teeth.

-CryptoLutheran

And what exactly is this common ancestor from which Chimps and Hums diverged? Show me....

"the divergence between the ape line and the old world monkey line"

And what is THIS common ancestor? Show me....

 

[ViaCrucis]

And what exactly is this common ancestor from which Chimps and Hums diverged? Show me....

"the divergence between the ape line and the old world monkey line"

And what is THIS common ancestor? Show me....

The exact species from which our lineages descended and share as a common ancestor is not, at this point, known.

I'm related, indirectly, to Dr. Samuel Mudd; the physician who patched up John Wilkes Booth's leg after he broke it the night he shot President Lincoln at Ford Theater. The line of Mudds which produced my great-grandfather isn't descended from Sam Mudd, but both lines of Mudds can be traced back to Maryland in the mid 18th century. I don't know who the common ancestor of the Sam Mudd line and the line of Mudds from which my great-grandfather was descended is. That particular piece of information isn't one I have. That there is a relationship, however, and a shared heritage can be ascertained by all the available evidence. I don't need to know who the specific individual was to know this much; though knowing that would certainly add more information to the picture as a whole.

-CryptoLutheran

 

[USincognito]

humans also have genes for feathers development. does its means that humans evolved from birds?:

Humans do not have genes for feathers. That would be a violation of the nested hierarchy.

 

[pshun2404]

The exact species from which our lineages descended and share as a common ancestor is not, at this point, known.

I'm related, indirectly, to Dr. Samuel Mudd; the physician who patched up John Wilkes Booth's leg after he broke it the night he shot President Lincoln at Ford Theater. The line of Mudds which produced my great-grandfather isn't descended from Sam Mudd, but both lines of Mudds can be traced back to Maryland in the mid 18th century. I don't know who the common ancestor of the Sam Mudd line and the line of Mudds from which my great-grandfather was descended is. That particular piece of information isn't one I have. That there is a relationship, however, and a shared heritage can be ascertained by all the available evidence. I don't need to know who the specific individual was to know this much; though knowing that would certainly add more information to the picture as a whole.

-CryptoLutheran[/QUOTE}

You made the claim there is one with no evidence. Now I know all the standard rhetoric used to evade the truth and make the made up story appear to supported but it is not and "No One Knows" diddly squat. I have had Ph.Ds give me examples of possible candidates and defend them all the time not realizing they contradict others who give different examples (they all ultimately fail). At this time at least it is hypothesis based assumption and has no place in being taught as an obvious fact.

 

[ViaCrucis]

You made the claim there is one with no evidence.

Not knowing the precise identity of the shared common ancestor doesn't change the fact that there was a common ancestor which is ascertainable by the evidence we do have. We don't need to know the identity of the grandfather of two sets of cousins to know that they are cousins and share a common grandfather. Or would you suggest that if the grandfather's name isn't known then cousins aren't cousins? Because that would be ostriching.

-CryptoLutheran

 

[pshun2404]

Not knowing the precise identity of the shared common ancestor doesn't change the fact that there was a common ancestor which is ascertainable by the evidence we do have. We don't need to know the identity of the grandfather of two sets of cousins to know that they are cousins and share a common grandfather. Or would you suggest that if the grandfather's name isn't known then cousins aren't cousins? Because that would be ostriching.

-CryptoLutheran

So you are saying that you believe humans grew out of an earlier ape lineage some 14 mya and that there is actual evidence you can show me that indicates this event?