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Author Topic:   Biological classification vs 'Kind'
BobTHJ
Member (Idle past 4988 days)
Posts: 119
Joined: 06-02-2010


Message 339 of 385 (565409)
06-16-2010 4:26 PM
Reply to: Message 318 by Coragyps
06-15-2010 10:01 PM


Edited by AdminModulous, : hidden off topic sections

This message is a reply to:
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BobTHJ
Member (Idle past 4988 days)
Posts: 119
Joined: 06-02-2010


Message 341 of 385 (565422)
06-16-2010 5:21 PM
Reply to: Message 323 by cavediver
06-16-2010 3:57 AM


Re: Getting down to details
Edited by AdminModulous, : Hid sections that didn't advance the discussion towards understanding Biological classifications vs 'Kinds'

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 Message 323 by cavediver, posted 06-16-2010 3:57 AM cavediver has not replied

Replies to this message:
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BobTHJ
Member (Idle past 4988 days)
Posts: 119
Joined: 06-02-2010


Message 342 of 385 (565423)
06-16-2010 5:23 PM
Reply to: Message 325 by Coyote
06-16-2010 9:47 AM


Re: And in reverse???
quote:
If you are positing H. ergaster to be a racial variant of H. sapiens that developed after the flood, and most likely after Babel, do you realize the implications?
You are proposing the exact same type of evolutionary change that scientists propose except thousands of times faster and in reverse!
Great observation! Why do I get the impression that you believe you caught me on some inconsistency?

This message is a reply to:
 Message 325 by Coyote, posted 06-16-2010 9:47 AM Coyote has seen this message but not replied

  
BobTHJ
Member (Idle past 4988 days)
Posts: 119
Joined: 06-02-2010


Message 344 of 385 (565426)
06-16-2010 5:34 PM
Reply to: Message 327 by Coyote
06-16-2010 10:45 AM


Re: Off the deep end
Edited by AdminModulous, : non advancing parts hidden - more tangents that need to be trimmed.

This message is a reply to:
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Replies to this message:
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BobTHJ
Member (Idle past 4988 days)
Posts: 119
Joined: 06-02-2010


Message 345 of 385 (565429)
06-16-2010 5:49 PM
Reply to: Message 331 by Taq
06-16-2010 11:24 AM


Re: Life Looks Evolved, Baraminology Looks Useless
quote:
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.
It is exactly what ERVs and shared pseudogenes demonstrate IF common ancestry is true. If however the baramin hypothesis is true ERVs and shared pseodogenes demonstrate something altogether different (similar creatures sharing similar design). There is more than one way if interpreting the evidence. My way IS logically consistent.
quote:
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?
A hypothesis is opinion. You examine the evidence and form an opinion about what that means. You then test it as you describe. The results of your tests then allow you to revise and improve your hypothesis - but it starts with an opinion (in this case Darwin's).
quote:
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)?
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.
quote:
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.
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.
quote:
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.
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.

This message is a reply to:
 Message 331 by Taq, posted 06-16-2010 11:24 AM Taq has replied

Replies to this message:
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BobTHJ
Member (Idle past 4988 days)
Posts: 119
Joined: 06-02-2010


(1)
Message 357 of 385 (565499)
06-17-2010 12:14 PM


First - I apologize sincerely to everyone for straying off topic. It was not my intent to violate the forum rules, but it is my responsibility to abide by them. For my breach of etiquette I am sorry.
Second - I leave today on a four day trip and it is unlikely I will be able to post during that time. During that time I intend to re-assess my level of involvement in this forum - It is consuming a disproportionate amount of my time. I'd really like to respond to each of your posts personally (I hate to leave questions or comments unanswered), but I'm not sure that's realistic. I don't want to cease my involvement entirely as I have enjoyed our conversations and have learned a lot in the process. My goal is to find a way to participate in a limited fashion while still fairly responding to the major questions and arguments that are raised.
Thank you all - I appreciate your taking the time to discuss these matters with me.

  
BobTHJ
Member (Idle past 4988 days)
Posts: 119
Joined: 06-02-2010


Message 368 of 385 (567152)
06-29-2010 7:32 PM


Replying to all outstanding messages here, sorry for the wait.
Taq in M340:
quote:
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.
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?
Taq in M346:
quote:
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.
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.
quote:
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
Please elaborate on 'EVOLUTIONARY MECHANISMS'. So called 'evolutionary distance' is primarily just a measure of genetic differences between species (part of the ontological model).
Percy in M350:
quote:
There's no point in discussing untested hypotheses. You prefer to believe that one day they'll replace current theory, and who knows, maybe you're right. But it would be perverse to argue that the currently available evidence supports your favored hypotheses, because it does not. It not only doesn't support them, it doesn't even suggest them. It is only the influence of Genesis that suggests them.
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.
quote:
One particularly significant difference of Borger's VIGEs from normal evolution is that it is directed. In his view evolution proceeded in a manner directed by prepositioned VIGEs rather than selected for by the environment. This doesn't explain adaptation. If evolution comes from within as directed by VIGEs with no input from the environment, how did adaptation ever occur?
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.
quote:
In other words, it makes sense to you that chimps are related to gorillas genetically, because they both had a common ancestor aboard the ark. And it makes sense to you that chimps and gorillas are related genetically to monkeys because monkeys shared the same common ancestor. But the same types of analysis that reveal this genetic relatedness show that the common ancestor was responsible for more than just monkeys. Rodents, and lizards and fish and insects and ultimately bacteria also share a common ancestor with chimps, gorillas and monkeys.
Again, you are assuming that genetic similarity implies common descent. Common descent is one reasonable explanation - but common design is another.
quote:
The animal kingdom is in pink, we're near the top. Select a lineage on the perimeter and trace inward toward the center, and this will take you through the branch points where lineages come together. Somewhere in these junctions you'd like to draw a line and say that it goes no further, that before that point the lineages possess no commonality and therefore had distinct origins. But there's no hint of this in the genetic analysis. If a designer is responsible for what you think are the original species, he designed in a nested hierarchy
I'm not at all suggesting no commonality. I don't argue against the genetic commonality of all life - I actually find this to be rather solid evidence for common design.
quote:
I think you've been misinformed. There's nothing in evolutionary theory that predicts that bacteria should require a great deal of time to evolve. What evolution predicts is that imperfect reproduction will cause genetic changes to accumulate over time. The shorter the generations the faster genetic changes can accumulate.
Agree. However, for the full traditional darwinian evolutionary process to occur - even in a rapidly reproducing organism - would still require a considerable amount of time. Consider the steps:
1. Gene duplication
2. A mutation event that deactivates the duplicated gene (thus allowing it to freely mutate)
3. A series of mutation events to modify the protein coded by the gene - as well as modifications to the regulatory elements that control expression for that pseudogene.
4. A mutation event that re-activates the new gene for expression.
At a minimum you must admit that the above process does not allow for the rapid evolution we have witnessed in bacterial studies. What has been observed is the activation of pre-existing dormant pseudogenes.
quote:
Using the link you provided, please read your reference and then post a message explaining how transposons support Borger's hypothesis that the VIGE ancestors of these transposons directed the course of evolution, as opposed to selection based upon the environment. It must be true that environmentally influenced selection could not have been a factor because with accelerated evolution the environment could not have been rapidly changing at the same time. Or did ancient historians not only fail to note the rapid changes in the local flora and fauna, but also that one year they were living in a forest, the next in a desert, and the next in a tundra.
Certainly (as stated above) environmental selection would play a major role. The flood event (and resulting continental drift) would cause some rapid environmental change. Species spreading into new areas of the now-unihabited world would also provide rapid exposure to new environments.
Also please understand I'm not suggesting high-orders of evolutionary change. The primary evolutionary change I am advocating for is exactly environmental adaptation. Historians wouldn't witness dinosaurs morphing into birds in a matter of a few generations - they would be able to see some minor variations in doves/pigeons as they speciated and adapted to the various environments they expanded into.
WoundedKing in M354:
quote:
One big problem is that Bob seems to be conflating the 2 different concepts of redundant and non-essential genes. The paper (Winzeler et al., 1990) (you don't need a subscription, but you do need to register with the Science website) discusses the effect of several hundred gene deletions and notes that most of these genes are non-essential, meaning that when they are deleted these genes do not cause a complete loss of viability. Of these non-essential genes 8.5% had more than one homologue in the genome, what we might consider gene redundancy. Of the essential genes, those whose deletion caused a complete loss of viability, only 1% had any homologues in the genome. So we can see that gene redundancy seems overrepresented in non-essential compared to essential genes, which seems to me to run totally counter to BobTHJ's claims.He seems to be trying to represent the research as if all of the non-essential genes should have duplicates to be in accord with current evolutionary theory.
What I was referring to is that the study demonstrates 83% of genes to be non-essential to survival, and of those 60% have no noticeable phenotype. Now, given - phenotypes may exist for some which were not found - for the sake of argument let's assume half of those 60% of non-essential genes would have a phenotype that reduces fitness in the wild (far more than is likely). That still leaves approx. 25% of the expressed genes in Yeast that HAVE NO PHENOTYPE and thus grant no additional fitness.
How does natural selection conserve genes that convey no fitness? The explanation was "those genes are the result of gene duplication", but the study shows this to be the case for less than one in ten.
Granny Magda in M355:
quote:
It is relevant because according to most creationist lists of "kinds" birds and dinosaurs are of different kinds. These fossils - transitional fossils - show that in reality, there are intermediate forms between the two kinds, that they are related. This destroys the idea of kinds, or at the very least, forces the kinds to be so flexible that they are meaningless and so accommodating that it is ever harder to see how humans and chimps can occupy separate kinds.
If conclusive evidence of feathered dinosaurs were shown this would not invalidate kinds. It would fit a new taxon between birds and dinosaurs - likely a separate extinct baramin (or baramins).
quote:
They are not assumptions at all, reasonable or otherwise. An assumption would be something taken as a founding axiom, in the absence of evidence. These findings are based upon careful scrutiny of the evidence; remember, evidence is not biased!
Conclusions based on evidence are assumptive in nature - because we never have full evidence. To use our example the evidence in question is several distinct fossils. We can draw reasonable conclusions from these fossils (and maybe feathered dinosaurs is a reasonable conclusion) but that conclusion requires a certain level of assumption - because there is much that remains uncertain.
quote:
By the way, as Percy has pointed out above, it doesn't matter how we construct our tree of life - genetic, morphological, whatever - we end up with pretty much the same nested hierarchy that Linnaeus observed centuries ago.
This agreement between genetic and morphological systems need not exist in a non-evolutionary world, but it does exist. It is a powerful vindication of Darwin.
As I've stated previously, I agree that the ontology based on genetic and morphological similarity models life with greater than 95% accuracy. This agreement does nothing to vindicate darwin (who made an assumption/conclusion of common ancestry based upon morphological evidence) it merely demonstrates that life shares much similarity.
quote:
Ultimately, it's down to what the evidence is telling us. Evidence is not biased. Follow the evidence and you will always be headed in the right direction. After all if you are right and the world is God's creation, then you will only be revealing the truth of his handiwork. If I am right, the evidence will show this too. I trust that you will be honest and forthright enough to do this.
I agree wholeheartedly - and can state with certainty that my YEC belief is a result of the evidence (at least the evidence I have seen).
quote:
Can't you see how those two comments contradict each other? The baramin must be objective. We agree on that. But if the baramin cannot be falsified, how can it be objective? An unfalsifiable idea can never be objective; it could be true or untrue, we would have no way of knowing. What point is there in having a classification so lax that it could be changed according to whim? What purpose would it serve? Any system of taxonomy must be objective. falsifiability is a big part of that.
I'm not contradicting myself here - let me see if I can explain more fully:
A hypothesis that isn't falsifiable isn't necessarily incorrect. It is however of limited use to objective science until a method of falsification is devised.
Specific baraminological hypothesis are falsifiable. The science as a whole would also be falsified if humans and chimps (or some other primate) were shown to have common ancestry.
Dr. Adequate in M358:
quote:
When creationists find it necessary to put forward arguments that undermine the possibility of us acquiring any knowledge at all, in order to deny our knowledge about evolution in particular, I think they're on the ropes.
This, of course, is not what I said. Thanks to our Creator we do have a tremendous capability to use our senses to acquire knowledge (which in itself is powerful argument against non-intelligent design). We can learn about what we observe. This however does not mean we ever fully understand anything - we only understand that which we have observed about it.
Just to set the record straight: I am not in any way suggesting that a spiritual enemy 'fixed' our observations (Though Granny's new avatar is cute) - evidence is evidence. I am suggesting that a spiritual enemy might influence the conclusions drawn from those observations. This is of course opinion on my part and should in no way be construed to be anything else.
articulett in M359:
quote:
Do you think that the theory of gravity LOOKS true because it stems from an effort to explain god's means of keeping the planets in orbit or "why things fal"l --without invoking god? What about germ theory? Atomic theory? Heliocentrism? The notion that the earth is an oblate spheroid rather than flat? (Remember, scientific theories are the best explanations for the observed facts.)
Scientific theories are the best explanation for the observed facts in the opinion of the one adhering to the theory.
quote:
To a scientist, "kind" is a vague term that allows believers to change the meaning as need be to fit whatever it is they feel saved for believing in. To understand more, we use more specific terms. "Kind" is used by people who want to remain purposefully ignorant of the facts so that they can continue to believe in the story they feel "saved" for "believing in". It's not a term used by those seeking to understand the actual origin of the species.
I falsify this hypothesis.
Percy in M360:
quote:
Oh, is that what "Homo holobaramin" means? Human? I didn't realize you were claiming that YEC scientists had predicted Neanderthals were human. So this would be a great example of the application of baraminology. How did they apply the principles of baraminology (which you have yet to describe, so this would be a great opportunity) to make this prediction?
Two means led to this prediciton. First, neanderthal fossils have been found with evidence of civilized society. Since baraminology dictates that only humans are sentient and capable of this level of societal organization, then neanderthal must be human.
Secondly, baraminological distances were compared between neanderthal and human fossils indicating a close correlation between the two. Sorry, I can't give great detail on this process as I don't clearly understand it yet.
quote:
By the way, the genetic analyses that indicate cross breeding between Neaderthals and humans (the criteria you're using to decide they were human) also indicate that the two lineages split about 500,000 years ago. So you think scientists are 1000 times off on some things but can be trusted on the rest? What criteria are YEC's applying to make these vastly different assessments of reliability of data from these closely related studies?
As mentioned in other posts YEC baraminology predicts much faster 'evolution' (adaptation and speciation) than would be found under a darwinian model. No doubt the 500k year estimate you refer to was based on the darwinian timescale and derived either from radio-isotope dating of fossils or from genetic differences and assumed mutation rates.
quote:
You misunderstood John Woodmorappe's description of the article. The article argued that Home egaster *does* belong in the genus Homo, while other lineages like Homo habilis do not. It wasn't arguing that Homo egaster should be reclassified as Homo sapiens.
Yes...sorry if I wasn't more clear. The homo genus is roughly equivalent to the YEC human holobaramin - ie 100% human 0% ape from a YEC perspective.
articulett in M361:
quote:
The fact that some humans contain Neanderthal DNA does not mean that humans descended from Neanderthal. It only means that there was some mating going on after the two lineages had split.
Horses and Zebras share a horse-like ancestor and can still produce offspring. (So can donkeys and zebra). But one did not descend from the other. We consider them separate species because their hybrid offspring are generally infertile and they do not mate in the wild.
Dogs, however, did descend from wolves and are considered a subspecies of wolf since they can still mate with and produce viable offspring with wolves. Even though the various breeds of dog look like separate species from each other, they are the same species. There are many species that look identical to other species (especially in plants and insects), but genetics shows that they are, in fact, different species.
"Kind" tends to be a term creationists play fast a loose with in order to make facts fit their predetermined conclusion. I have a Masters in Genetics, and I don't know any scientist that uses that term, nor have I ever heard of the "baramin hypothesis".
I wasn't implying neanderthal were human ancestors - an extinct species of the human baramin is more accurate. However, you give some good examples and thus allow me to state the following falsifiable hypothesis (which I've been considering and did not originate with me):
Interbreeding (even under laboratory conditions) can be used as an inclusive test to determine if an organism lies within a certain baramin.
Note that when interbreeding was discussed at the beginning of this thread by those attempting to characterize baraminology it was done so in an exclusive manner: "if two organisms can't interbreed then they are in separate baramins". This does not hold true however due to speciation (organisms that were once able to interbreed may no longer be able to due to chromosomal reconfiguration or phenotopic incompatibility). However, if two organisms CAN interbreed then the baraminologist can reasonably conclude that they ARE in the same baramin. This includes interbreeding under laboratory conditions (up to but not exceeding manual alignment of chromosomes for meosis) and is valid even if offspring do not remain viable until maturity.
This hypothesis can be falsified if a human/chimp interbreeding could be accomplished in the laboratory.
According to this hypothesis (and using your examples) horses and zebras are part of the same baramin. Dogs and wolves also share a baramin. Finally humans and neanderthal's share a baramin.
I'm trying to get as far away from 'fast and loose' here as I can...
articulett in M365:
quote:
How does a biblical literalist explain this. Did god take some sheepish goatish ancestor on board and do super fast evolution to make these two different species or did he just poof out two separate but similar-enough-to-breed species and have them board the ark in pairs? These appear to be separate "kind" to people writing the bible since they have separate names for sheep and goats. And what about Kangaroos and wallabies which they didn't even seem to know about? And how did they get to Australia from Mount Ararat? Why are there no fossils of marsupials in the middle east?
You're not asking any tough questions here... rapid speciation from a sheep/goat common ancestor is certainly possible - and I've demonstrated the means (VIGEs - see the baranome hypothesis I posted about here and on the genetic redundancy thread). A global flood event as hypothesized by YEC would generate the continental drift from pangaea to (almost) present form thus allowing for rapid re-population of the planet and explaining how specific kinds may be found all or only certain continents.

Replies to this message:
 Message 369 by Taq, posted 06-30-2010 12:47 AM BobTHJ has not replied
 Message 370 by Wounded King, posted 06-30-2010 4:57 AM BobTHJ has not replied
 Message 371 by Peepul, posted 06-30-2010 10:27 AM BobTHJ has not replied
 Message 372 by Granny Magda, posted 06-30-2010 1:00 PM BobTHJ has not replied
 Message 379 by Coragyps, posted 06-30-2010 10:02 PM BobTHJ has not replied

  
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