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Author Topic:   Biological classification vs 'Kind'
Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 299 of 385 (565072)
06-14-2010 4:21 PM
Reply to: Message 297 by BobTHJ
06-14-2010 2:57 PM


Re: Life Looks Evolved, Baraminology Looks Useless
False. Most every new organism discovered fits well into an ontology for classifying organisms according to similarities.
Why would different baramins share any features at all? There is no reason for them too. Why should the human and ape baramine share any features, much less 98% of the DNA? Why should mammals and bacteria use the same tRNA codons if they were created separately?
Not surprisingly, most genetic evidence also fits because organisms with similar morphological features often share similar genetic features.
Again, why isn't this surprising? Isn't this exactly what we should see if common ancestry is true? Or are you saying that we should throw out every DNA paternity test ever done because the two people could have been magically poofed into being?
Darwinists just make the jump from there that the nice ontological model implies a common ancestry of all organisms - a claim for which there isn't much evidence.
If common ancestry is true should we or should we not observe a nested hierarchy? Since we observe a nested hierarchy, why isn't this evidence of common ancestry? Is your only refutation, "Well, they could have been magically poofed into being"? Is your only refutation a what-if fantasy based on supernatural magic?
I was stating that the YEC model (and its hypotheses) are based upon an interpretation of the Bible.
This is in stark contrast to the theory of evolution which is based on the empirical evidence.
You wouldn't suggest that the ToE is unscientific simply because it originated from Darwin would you?
It originated from the evidence that Darwin discovered on his journeys, most notably on the HMS Beagle.
Flawed reasoning. There is no causation between naturalism and scientific advance.
Can you name a single scientific advancement that is solely based on divine revelation? From my knowledge, the scientific advances we have today are the product of methodological naturalism, not divine revelation.
The dismal track record of supposed transitional "human ancestor" fossils over the years doesn't help you here. If the consensus among other posters is that an examination of those fossils is on-topic then I'd be happy to discuss them in more depth.
What dismal track record? We have more hominid fossils than we ever had the right to expect to have. Using the letters next to each skull can you tell us which belong to the ape baramin and which belong to the human baramin?
For those of us who do subscribe to Baraminology - it is important to identify the limits of a baramin.
Important for what? Apologetics?

This message is a reply to:
 Message 297 by BobTHJ, posted 06-14-2010 2:57 PM BobTHJ has replied

Replies to this message:
 Message 326 by BobTHJ, posted 06-16-2010 10:33 AM Taq has replied

  
Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 309 of 385 (565234)
06-15-2010 4:09 PM
Reply to: Message 303 by BobTHJ
06-14-2010 7:13 PM


This would seem to add evidence for the baranome/VIGE hypothesis. Which came first? The chicken or the egg? The ERV or the retrovirus?
Which came first, meteors or the craters on the moon? Obviously, retroviral activity came first since the ERV's carry the genes necessary for integration into the genome, reverse polymerase, and capsid proteins necessary for making a viron. ERV's are without a doubt the result of retroviral insertion SINCE THAT IS WHAT RETROVIRUSES DO.
If you want to claim that they were magically poofed into the genome by a supernatural deity then it is incumbent on you to supply the observations.

This message is a reply to:
 Message 303 by BobTHJ, posted 06-14-2010 7:13 PM BobTHJ has replied

Replies to this message:
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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 311 of 385 (565240)
06-15-2010 5:00 PM
Reply to: Message 301 by BobTHJ
06-14-2010 6:43 PM


Re: Insults?
Yes you already know the answer. This is simply proof that there is more than one way semi-coherent way to interpret the evidence.
It is proof that the only reason one would conclude that the Earth is young is if their religious beliefs require it. Why else would you suggest that the Earth is young? Your "semi-coherent interpretation" requires us to throw out every known fundamental law of the universe, from radioactive decay to the speed of light. How is that semi-coherent? If you were defense attorney would you claim that leprechauns planting your client's fingerprints at the scene of the crime is a "semi-coherent interpretation of the evidence"? If not, then why is the unevidenced magical manipulation of the forces of nature any more coherent when it comes to young earth creationism?
1) Is it (to a high degree) internally consistent?
The problem is that YEC is not externally consistent. It is inconsistent with the evidence we find the external world.

This message is a reply to:
 Message 301 by BobTHJ, posted 06-14-2010 6:43 PM BobTHJ has replied

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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 312 of 385 (565243)
06-15-2010 5:06 PM
Reply to: Message 310 by BobTHJ
06-15-2010 4:49 PM


Re: a deeper understanding
Borger's hypothesis is that the mobile genetic elements we see today are what's left of VIGE's. Many seem to have been damaged by 6k+ years of mutation and so don't function as originally intended.
1. What evidence, if found, would falsify Borger's hypothesis.
2. How did Borger determine what the original intention for these genes was.
3. How did Borger determine that "damage" started to accumulate in these genes just 6k years ago.
There is circumstantial evidence - the ability of organisms to rapidly adapt and evolve - far faster than darwinian evolution would predict.
Examples?
The current level of diversity in life we witness today matches with the 4500 year timeframe since the flood - assuming base kinds were transported on the ark.
Evidence please.
As cryptic genes are not expressed to make any positive contribution to the fitness of the organism, it is expected that they would eventually be lost due to the accumulation of inactivating mutations. Cryptic genes would thus be expected to be rare in natural populations. This, however, is not the case. Over 90% of natural isolates of E. coli carry cryptic genes for the utilization of beta-glucoside sugars. These cryptic operons can all be activated by IS [insertion-sequence] elements, and when so activated allow E. coli to utilize beta-glucoside sugars as sole carbon and energy sources
Sounds to me that natural selection is keeping these genes around.
It is quite possible that similar organisms all shared very similar genes with the functional differences being in how and when those genes were expressed.
Evidence please.
No, I don't have any evidence - I was postulating.
The problem here is that you are rejecting explanations backed with tons of evidence in favor of your unevidenced postulations.

This message is a reply to:
 Message 310 by BobTHJ, posted 06-15-2010 4:49 PM BobTHJ has replied

Replies to this message:
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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 330 of 385 (565365)
06-16-2010 11:16 AM
Reply to: Message 322 by BobTHJ
06-16-2010 3:44 AM


Re: Getting down to details
But there are aquatic and flying mammals that both use echolocation. And when I brought that up you told me that we don't classify based on a single feature but on the overall similarity. Based on overall similarity I could build a nested hierarchy of vehicles.
Echolocation is not a morphological feature. It is a behavior.
Yes there is....common design.
There is no reason that an omnipotent and omniscient supernatural designer would reuse designs. For an all powerful being starting from scratch involves the same effort as reusing design. Therefore, there is no expectation for common design.

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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 331 of 385 (565367)
06-16-2010 11:24 AM
Reply to: Message 326 by BobTHJ
06-16-2010 10:33 AM


Re: Life Looks Evolved, Baraminology Looks Useless
This is bad logic. Yes common ancestry requires a nested hierarchy, and yes we seem to have an ontological model that looks very similar to a nested hierarchy.
It is more than very similar. It is a nested hierarchy.
However, you need more than that to prove common ancestry - if this weren't the case then scientists would have no reason to go "hoopla!" every time they find a so-called transitional fossil. They are desperate for something to support this massive assumption.
And that is exactly what ERV's and shared pseudogenes demonstrate: common ancestry. You continue to ignore this evidence in favor of made up fantasies.
Complete nonsense. The theory of evolution is based upon the opinions of Charles Darwin (and others).
Island endemism, biogeography, the nested hierarchy, new variations produced by artificial selection, fossil sorting in the geologic record, and many more facts were used by Darwin to support his theory. It is much more than opinion, and you know it. Not only that, I have shown time after time how the theory of evolution makes specific and testable predictions, and those predictions bear out in experiments. With all of this how can you claim that it is just opinion?
I'll reference AiG's list of creationists agian - if you scroll down you will see that many of the scientists who made significant advances in modern science were creationists.
How many of them made advances in modern science using baraminology in their research? And how many are named Steve or derivations thereof (I will explain this later)?
If you'd like to discuss this I am happy to. Let's take them one at a time. You pick.
I asked first. Using the letters next to the fossils please tell us which species belong to which baramin, and please list the objective criteria that you used to determine this.
For the continued advancement of science. If/when the day comes that common ancestry is discarded as a viable theory it would be nice to have some of the classification work of baramins complete so no further time is wasted.
As I have already shown, the common ancestry model combined with evolutionary mechanisms is extremely useful and has born fruit. Creationists have been working on baraminology for 50 years and it has born exactly zero fruit. It would seem that the creationists are the ones wasting their time.

This message is a reply to:
 Message 326 by BobTHJ, posted 06-16-2010 10:33 AM BobTHJ has replied

Replies to this message:
 Message 345 by BobTHJ, posted 06-16-2010 5:49 PM Taq has replied

  
Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 340 of 385 (565416)
06-16-2010 4:42 PM
Reply to: Message 338 by BobTHJ
06-16-2010 4:07 PM


Re: a deeper understanding
1) Evidence of new genes creating significant new function not previously found either active or dormant within the genome.
A bit of a catch-22, isn't it? If a new gene does evolve through mutation you will claim that it was a dormant gene. You have already claimed such for EBG (evolved beta-galactosidase gene) in the Hall study.
2) Evidence that mobile genetic elements (VIGEs) are and always have been "selfish" and random.
Retroviruses and transposons do have preferences for certain kinds of sites in the genome, but these sites are very plentiful, made up of many bases, and the preference for these sites is not 100%. Therefore, these preferences do not interfere with the phylogenetic signal. Also, what is stopping evolution from making a solo LTR into a functional gene in the genome?
Borger didn't determine anything. He is postulating. This is a hypothesis.
So what experiments can you do to test these hypotheses? What experiments can you do to determine when these sequences started accumulating mutations? What experiments can you do to determine their original function and intent?
Please explain how there is positive selective pressure for an unexpressed gene?
The selective pressure was on the previously functional gene which is restored through mutation. You should read up on the SOS mechanism in E. coli. When the bacteria sense DNA damage (usually caused by starvation) the bacteria turn on genes that code for recombinases and error-prone polymerases. This results in a huge upswing in gene duplication and mutations. This is how these genes are kept around.

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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 343 of 385 (565424)
06-16-2010 5:29 PM
Reply to: Message 341 by BobTHJ
06-16-2010 5:21 PM


Re: Getting down to details
Edited by AdminModulous, : off topic section hidden (or at least, its wandered so far it threatens to create drift)

This message is a reply to:
 Message 341 by BobTHJ, posted 06-16-2010 5:21 PM BobTHJ has not replied

  
Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 346 of 385 (565430)
06-16-2010 6:07 PM
Reply to: Message 345 by BobTHJ
06-16-2010 5:49 PM


Re: Life Looks Evolved, Baraminology Looks Useless
It is exactly what ERVs and shared pseudogenes demonstrate IF common ancestry is true.
You have things completely backwards.
Imagine you are a defense attorney in a murder trial. The prosecution presents DNA, fingerprints, shoe print, tire tracks, and fiber evidence all of which links your client to the murder and the scene of the crime. Would you approach the jury and proclaim that all of this evidence indicates guilt, but only if your client were truly guilty. You then proclaim that your client is not guilty, so they should just ignore all of this evidence. In fact, there is another explanation. The evidence is also consistent with an evil spirit who wants revenge on your client. You even go as far as to claim that this is a reasonable explanation, much more reasonable than your client actually committing the crime.
Does this sound reasonable to you? This is the argument you are using.
There is more than one way if interpreting the evidence. My way IS logically consistent.
We do not observe supernatural deities incorporating retroviral sequences into genomes. We do observe retroviruses inserting their genome into the host genome. We do observe that the 5' and 3' LTR's of and inserted retroviral sequence are identical at the time of insertion, but that these sequences have diverged over time in the genomes of the host. We do observe that retroviruses insert randomly among billions of bases meaning that the chances of two insertions occuring at the same base are highly improbably. We observe that the same ERV's (thousands of them) are found at the same base in multiple species. We observe that common ancestry produces a nested hierarchy.
Now please tell me how magical poofing is more logical than real observations of nature.
A hypothesis is opinion.
Bullshit. A hypothesis is a testable and verifiable statement. An opinion is not.
I do not know the answer to either of these questions. Baraminology (as we've discussed) is not a well-developed science yet - so the answer to your first question may be none. You are certainly welcome to do the research to answer your second question, you haven't given me any reason to take the time out of my day and do it.
Why haven't you done the research? You are calling for the expulsion of common ancestry for a supposedly better system (baraminology) and yet you don't even know if either is being used or is well developed. I do know. Common ancestry and evolution are immensely useful in biological research, and baraminology (which has been around for 50 years) is an abject failure. So please tell us why you want to replace a model that works with one that doesn't.
I don't wish to participate in this game. If you'd like to discuss so-called transitional fossils on a case by case basis then name one and we'll get started.
You claim that humans and apes are in separate baramins. Time to prove it. If you can't then withdraw the claim.
I don't recall you showing anything of the sort. The SIFTER research was the closest - but that was based on an ontological model and had nothing to do with common ancestry.
No, SIFTER is based on an evolutionary model that incorporates common ancestry and divergence over time. At least try to be honest about other people's work. SIFTER uses EVOLUTOINARY DISTANCE and EVOLUTIONARY MECHANISMS to predict protein function. It doesn't use an "ontological model", it uses an evolutionary one. And SIFTER is the tip of the iceberg. SIFTER is a program based on the methodology of phylogenomics. A search for phylogenomics and http://www.pubmed.com will turn up hundreds of papers that use the theory of evolution to better understand the function of genes and proteins. No one, and I mean no one, is using baraminology.

This message is a reply to:
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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 347 of 385 (565431)
06-16-2010 6:11 PM
Reply to: Message 344 by BobTHJ
06-16-2010 5:34 PM


Re: Off the deep end
Edited by AdminModulous, : more trimming.

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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 369 of 385 (567188)
06-30-2010 12:47 AM
Reply to: Message 368 by BobTHJ
06-29-2010 7:32 PM


I guess I'm not understanding how this allows selection to preserve a non-expressed gene over time. Can you explain further? or point me to some reading material?
Because selection is able to restore the function of the gene faster than genetic drift (aka no selection) is able to take the function away. To use a rough analogy, it is a bit like a dog on a leash. The dog slowly starts to wander off, but a well directed tug brings them back to your side in a jiffy. The wandering is analogous to unselected genetic drift while the tug is positive selection.
Where did the retro-virus initially come from? Even in a darwinian model it is not unreasonable to suspect that the first retro-viruses were spawned by a mutated section of transposable DNA in a different organism.
Where viruses came from is still a hotly debated topic. IMHO, the best candidate is an ancient unicellular obligate parasite not too different from the ubiquitous chlamydia species that we see today. In fact, there are lifeforms such as mimiviruses which carry very large genomes (for a virus) that may demonstrate a link between the small genomes of retroviruses and the larger genomes of bacteria. I would suspect that viruses have been around for almost the entire history of life. They are the epitome of selfish DNA.
Borger's hypothesis (which I've since learned appears to have been put forward - at least in part - much earlier by Todd Wood) does fit the evidence we currently observe - if it does not please demonstrate how.
What potential observation would Borger's hypothesis not fit? How does Borger's hypothesis explain LTR divergence? How does it explain overall ERV divergence? To be more specific, why do ERV's that are shared by orangutans and humans at orthologous positions have a higher LTR divergence than orhtologous ERV's shared by just chimps and humans? Why does the overall ERV divergence fit the same pattern? How does Borger's hypothesis explain this? How does Borger explain how a whole family of viruses can be found in chimps and gorillas but not in orangutans and humans, and at the same time why don't we find any of these ERV's at orthologous positions in chimps and gorillas (see this paper)? If you are going to claim that Borger's hypothesis explains the observations then it MUST explain these observations. Common descent with modification (i.e. evolution) DOES explain these observations. In fact, if common ancestry and evolution are true then we SHOULD observe these relationships.
Please elaborate on 'EVOLUTIONARY MECHANISMS'. So called 'evolutionary distance' is primarily just a measure of genetic differences between species (part of the ontological model)
It is also established by the fossil record which the ontological model can not explain.
Borger isn't arguing against selection by environment. Directed VIGE transpositions activate dormant psuedogenes causing new phenotypes - and natural selection then chooses the most fit phenotypes for the environment. Borger also hypotheses VIGEs that serve other function (modifying chromosomal configurations to prevent interbreeding and thus force speciation) but this is in addition to the first function, not in place of.
Can you please show where Borger explains why humans need reverse trascriptase and viral capsid proteins.
Again, you are assuming that genetic similarity implies common descent. Common descent is one reasonable explanation - but common design is another.
Then please list the similarities that the phonograph and light bulb share. Please show how Stephen King's novels fall into a nested hierarchy. Please show how airbags are only found in a single lineage of cars, the lineage of cars that airbags were first observed. Please explain why the similarities you share with your siblings is not due to common descent, but due to magical poofing (I am sure that your parents would be really interested in this one).
The flood event (and resulting continental drift) would cause some rapid environmental change.
So would a major meteor impact 200 years ago, but there is no evidence that either happened.
If conclusive evidence of feathered dinosaurs were shown this would not invalidate kinds.
What would? Anything? If any possible evidence fits with baraminology then how can you claim that the evidence convinced you?
Conclusions based on evidence are assumptive in nature - because we never have full evidence.
So you accept creationism with zero evidence, but you reject evolution because we don't have complete knowledge of everything that has ever happened in the entire universe. Color me surprised.
Finally humans and neanderthal's share a baramin.
How did you establish this?

This message is a reply to:
 Message 368 by BobTHJ, posted 06-29-2010 7:32 PM BobTHJ has not replied

  
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