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Author Topic:   Biological classification vs 'Kind'
Taq
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Message 56 of 385 (562948)
06-02-2010 4:26 PM
Reply to: Message 55 by BobTHJ
06-02-2010 4:17 PM


It is logical from a YEC standpoint to assume that God created a base Gull kind, but since creation the two extremes of that baranome have diverged to the point to not allow hybridized offspring.
So why not have a base Ape kind from which humans, chimps, gorillas, and orangutans have diverged from? Why not a base Primate kind, a base Mammal kind, or a base Vertebrate kind? Where is the dividing line, and what objective criteria are you using to draw this line? What genetic characteristics should not be shared by separate kinds? What physical characteristics should not be shared by separate kinds?
The issue is not "Does natural selection acting on mutuation cause adaptation?" (we agree on that) but instead "Did the process of evolution begin 4 billion years ago with a single-celled organism or 6-10 thousand years ago when God created distinct kinds of creatures?"
Is this issue based on religious beliefs or science?
The term "macroevolution" seems to have a loose definition among creationists - but I typically take it to mean common descent from a single ancestor. I don't know that creationists spend a lot of time defining it since we don't subscribe to it.
If creationists don't know what macroevolution is then how can they claim it doesn't happen?
I do know there has been an effort made by Answers in Genesis and others to abandon the term and instead use "molecules-to-man evolution" because it better describes the concept.
It doesn't come close to describing the concept that humans share a common ancestor with other apes.

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 Message 55 by BobTHJ, posted 06-02-2010 4:17 PM BobTHJ has replied

Replies to this message:
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Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


Message 60 of 385 (562955)
06-02-2010 5:23 PM
Reply to: Message 58 by BobTHJ
06-02-2010 4:56 PM


A base kind for wider classifications (primates, mammals, or even vertebrates)? Theoretically possible in a YEC model but highly unlikely given the timeframe (7-10k years) for such adaptation to occur.
So then kind is limited to the observed mutation rate and a 10k year old Earth? What about Old Earth Creationists?
As BlueJay pointed out earlier how life is classified into kinds is far from an exact science - and there is some disagreement on the issue (just as there is in the classification of life under a darwinian model).
The inexactness of a cladogram is proportional to amount of phylogenetic data available. However, what is observed again and again is a continuity of the biological classifications, a continuity that doesn't make sense if kinds were created separately. Every primate is also a mammal. How does that happen? Why not a kind of animal that is part monkey and part bird that would prevent it from also being a mammal? It is the fact that we can form clades for large numbers of species that points away from creationism and towards shared ancestry.
Humans are of course a different animal entirely (no pun intended).
Every species is different, including species you would place in the same kind.
not sure how this is relevant to the topic of discussion - but if it's necessary to clarify: all science requires certain assumptions to be made.
I guarantee that the assumptions you are thinking of are not the assumptions that science makes.
Darwinian evolutionists tend to rule out any assumptions of a supernatural origin as non-science (perhaps because they are afraid of what that might mean?) and instead accept far more fanatical assumptions that fit a naturalistic model.
Without assuming the existence of the supernatural why would you ever mention it? It is you making the assumption. There is no evidence of the supernatural, so why include it in science? Science assumes that there will be a rational explanation backed by empirical evidence. Why is that such a horrible assumption?
I on the other hand prefer to make the most reasonable assumptions to fit the data - even if those assumptions may be supernatural in origin.
What makes the untestable and unevidenced supernatural a reasonable assumption?
As I said, there seems to be a lot of confusion over the term - hence the effort by some leading creationists to use a term that better describes the concept of common ancestry from a single organism.
What are the scientific experiments one can run to determine if two species do or do not share a common ancestor, according to creationists?
Agreed....can you think of a better term? It'd sure be nice to have a phrase that clearly explained the issue - I for one grow weary of constantly having to give lengthy explanations to darwinists who don't understand the basic principles of YEC science.
"Molecules to man" is designed to be derisive. The older term is "goo to you via the zoo". It is meant to muddy the waters by slopping together abiogenesis and evolution, two separate concepts. AiG and others know that they have already lost, so they are playing to the crowd. Think of it as two politicians calling each other names without ever spending time talking about policy or governance. AiG has no definition of kind, or any scientific methodology that would separate species into kinds. All they have is name calling. That should tell you a lot.

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 Message 58 by BobTHJ, posted 06-02-2010 4:56 PM BobTHJ has replied

Replies to this message:
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Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


Message 61 of 385 (562956)
06-02-2010 5:34 PM
Reply to: Message 59 by BobTHJ
06-02-2010 5:23 PM


As to why use the word "kind" instead of "clade" I also should probably defer to someone with more knowledge than myself - I honestly don't know. Perhaps they could be used interchangeably?
If they were used interchangeably then humans would be a part of the ape clade, the primate clade, the mammal clade, the vertebrate clade, and so forth. Clades are rooted by synapomorphies which are shared characteristics. Each branch from the root evolves derived characteristics. Humans share many, many characteristics with other apes, fewer with all primates, fewer still with all mammals, and so forth. The more time that has passed since common ancestry allows for more derived characteristics to evolve. This is exactly what we see in the characteristics of living species, in the fossil record, and the genomes of living species.
"Kinds" makes no sense. It can't explain why derived characteristics appear in the fossil record with time. It can't explain the relationships between pseudogenes and shared physical characteristics. It can't explain why humans share so many ERV's with other apes at the exact same spot in their genomes. "Kinds" explains nothing other than a need to keep humans separate from the rest of life due to religious beliefs. That's it.
I haven't seen any data yet that would indicate an ability for the evolutionary process to add any significant data to the genome - only to remove or rearrange.
The data is the comparison of the genomes between any two species. It clearly shows that the differences in DNA is responsible for the differences in physical characteristics. I would think that even creationists would agree with this. What I have yet to see is a creationist that can show us genetic differences that evolution could not produce, and why.
And to stray back to the topic, it would seem that you may have stumbled on a way to define kinds. Simply show which genetic differences evolution can not produce, and any species with those differences would automatically be in different kinds. So what genetic changes can evolution not produce? I would assume that the genetic differences between humans and chimps would be on the list, so could you give an example of a difference in a human and chimp gene that evolution could not produce?

This message is a reply to:
 Message 59 by BobTHJ, posted 06-02-2010 5:23 PM BobTHJ has replied

Replies to this message:
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Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


(1)
Message 129 of 385 (563152)
06-03-2010 3:14 PM
Reply to: Message 63 by BobTHJ
06-02-2010 6:09 PM


It makes quite a lot of sense for baraminology to look similar to the phylogenetic tree at the ends (furthest branches). YEC doesn't dispute the divergence of species since creation/flood. However your claim that the base of the phylogentic tree has continuity is quite false.
But we do see a continuity with all vertebrates, including humans. YEC and baraminology can not explain this. With YEC there is no reason that we should not see a feathered bat or a bird with three middle ear bones. There is no reason that separate baramins should fall into a nested hierarchy or clade. The only way this makes sense is if common ancestry is true.
For the base root of the tree it is convoluted due to horizontal gene transfer and endosymiosis, but for animals there is no such problem and the expected phylogenetic pattern is observed.
You're all mixed up here. Any science requires assumptions. Here's some of the common ones darwinian evolutionists make:
1. abiogenesis
2. uniformation in the geological record
3. a constant decay rate for radio-isotopes
1. and 2. are not the assumptions that science makes. Abiogenesis is not assumed, and is in fact an active area of research. All evolution needs is life, and the fossil clearly indicates that life existed so no assumption. The constant decay rate of isotopes is an observation backed by millions of data points and by quantum physics. 2. is assumed. Science does assume that the laws of nature are the same through space and time so when we see a chalk deposit forming today we assume that an identical chalk deposit in the past was formed the same way. What is wrong with that?
The goal with science is to examine the data and then make the most reasonable assumptions/predictions about that data.
No. The goal of science is to construct hypotheses that are then tested. How do you test for the supernatural? Specifically, what hypothesis can you form for the existence of baramins, and what evidence if found would falsify the hypothesis?
If the data strongly opposes all known naturalistic assumptions?
Then you look for other pathways. What you don't do is invent an untestable supernatural realm from whole cloth and claim it is the cause. That is not science.
Again, sorry....I'm not qualified to answer comprehensively at this point. Obviously comparison of genomes or mophological features are relevant indicators - but certainly not deciding factors (just as in a darwinian model).
Genetics and morphological data are more than enough to establish common ancestry.
LOL - It's not AiG that's slopping together abiogensis and evolution! As I've said several times now - we agree about evolution (in the natural selection/mutation/speciation/adaptation sense).
We do disagree. The fingerprints of evolution are all over the human genome, and they indicate our shared ancestry with the rest of life on this planet. You claim that there is a different fingerprint, but you are incapable of describing it. What is it?

This message is a reply to:
 Message 63 by BobTHJ, posted 06-02-2010 6:09 PM BobTHJ has replied

Replies to this message:
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Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


(1)
Message 132 of 385 (563156)
06-03-2010 3:27 PM
Reply to: Message 66 by BobTHJ
06-02-2010 6:46 PM


Those are all non-problems from a YEC standpoint - it would make sense that creatures with a similar morphological appearance would have similar genetic makeup.
Why would an all powerful and all knowing deity need to reuse any kind of design or genetic makeup? Isn't it just as likely that every single kind would have it's own genetic systems, or at least it's own codon usage? For an all powerful being reusing designs is just as easy as starting from scratch.
Also, why does the reuse of design fall into a nested hierarchy, into a clade? Why do bats have three middle ear bones and fur while birds have a single middle ear bone and feathers? Why should bats share more features with a fox than it does another flying creature? We don't see this pattern of shared characteristics when humans re-use designs. Human designs do not fall into a nested hierarchy. Even more, humans readily move genes between different species which violates the nested hierarchy. Again, the only explanation for this pattern of shared characteristics is common descent and evolution.
Think of a computer programmer - they don't code each program from scratch.
That's because humans do not reside outside of time and space and are not all knowing and all powerful.
As to the ERVs there is a reasonable explanation as well (though here I hesitate as I've only briefly reviewed the theories and research on this subject). The theory suggests that retroviruses are not the cause of the ERV genetic match - it's the other way around.
We observe retroviruses inserting themselves into genomes. We observe that they do this randomly. Therefore, when you see two insertions at the same spot in two different genomes the only explanation is that it is from a single insertion in a common ancestor. Also, the divergence of ERV sequences (both overall sequence and LTR divergence) produces the same phylogenetic tree as the placement in the genome. Three different sources of phylogenetic ERV data all point to the same thing, humans and other apes sharing a common ancestor. Your scenario does not explain these phylogenetic signals. For more reading go here.
Yes, I agree that comparing the DNA for two species will demonstrate the differences between those species. However, jumping from there to common ancestry of those two species is pure speculation
No, it is not speculation. The genetic evidence (such as the ERV evidence in the paper above) clearly indicates shared ancestry.
I'm not quite sure what that has to do with demonstrating the capability of the evolutionary process to add information to the genome.
Surely the different genomes contain different information, do they not? That different information is due to different sequences. Mutations produce different sequences, and selection filters out the bad and allows the good to prosper. If you disagree, then please pick two genomes from two different baramins and show us which differences evolution could not produce.
I know of no change that evolution is incapable of producing. I also however know of no change that evolution is capable of making that adds information to the genome.
Compare the genome of humans and chimps. Those differences are what evolution is capable of producing. It really is that simple.

This message is a reply to:
 Message 66 by BobTHJ, posted 06-02-2010 6:46 PM BobTHJ has replied

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Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


(1)
Message 135 of 385 (563166)
06-03-2010 4:20 PM
Reply to: Message 116 by BobTHJ
06-03-2010 1:21 PM


Re: Getting down to details
Now, certainly in some of the simple observational sciences where results can be observed and repeated in a labratory bias plays a minimal factor. But not so with origin sciences. Ancient history (whatever form it may take) can not be repeated and observed.
Past events create evidence that can be observed in the here and now. This includes fossils and inherited DNA. One can construct hypotheses and use this evidence to test the hypothesis. For example, if common ancestry is true then you should not find a fossil with feather impressions and three middle ear bones.
So what hypotheses can one construct using baraminology? What features would a fossil need in order to falsify baramins? What genetic features would one need to observe in order to falsify baramins? This is how you get rid of bias, by making risky predictions. Baraminologists refuse to make these risky predictions.
Bias tends to show itself most in the conclusions drawn form the data - take the example of the semi-recent discoveries of preserved soft-tissues in the fossil record. The darwinist's conclusion from the data was that some as yet unknown chemical process preserved the tissue for millions of years. This was based on their preconceived bias or "foundational truth" of molecules-to-man evolution.
That's false. It was based on the ratio of isotopes in the rocks surrounding the fossil. The age of the fossil is known and is solid. You can go measure the rocks yourself if you think their results are biased. The problem is figuring out how tissue can be preserved for about 65 million years.
Creation scientists on the other hand made the much more reasonable conclusion that the fossil was merely thousands of years of age.
Why is it more reasonable? Radioisotope dating has been tested through and through, and it is accurate.
Now, I understand that darwinists consider these assumptions to already be proven - but it is exactly this unwillingness to question the assumptions that leads to bad science.
Like you have already shown, you don't even know what these assumptions are. The assumptions of science (including the biological sciences) are rather mundane. First, there are knowable causes for natural phenomenon. Second, the universe is rational and can be examined by rational beings. Third, knowledge is gained through empirical observations. Fourth, nature behaves the same through space and time (uniformity). If water boils at 100 C today it will boil at 100 C tomorrow if the variables are the same. That's about it. The constant decay of radioisotopes is not assumed, it is observed. Abiogenesis is not an assumption, it is a field of research where nothing is assumed. Common descent is not speculation or an assumption, it is a conclusion drawn from hundreds of thousands of tested hypotheses.
And yes, while the mainstream scientific consensus at this point accepts those assumptions this does not mean Baraminology is a waste of time or effort.
What you seem to be missing is that evolution is USEFUL. Phylogenetics is a very important tool. In the field of comparative phylogenomics the theory of evolution allows one to use common ancestry and evolution to predict protein function, as one example. No one is using baraminology to do . . . well, anything (unless you count christian apologetics as something).

This message is a reply to:
 Message 116 by BobTHJ, posted 06-03-2010 1:21 PM BobTHJ has replied

Replies to this message:
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Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


(2)
Message 147 of 385 (563304)
06-04-2010 9:51 AM
Reply to: Message 143 by BobTHJ
06-03-2010 7:26 PM


For kinds of vertebrates to be grouped into larger classes is not at all an indication of common ancestry. The Bible speaks of larger classes of vertebrates as well. This just demonstrates order - an attribute of the Creator.
Since when is a nested hierarchy an attribute of the Creator?
It would be nice for you if there was the level of continuity to neatly fit every vertebrate into clades - but it's just not there. Consider the hundreds of cases of similarities in supposedly unrelated species conveniently explained away as convergent evolution (what a weak assumption!). Scientists can't even decide if birds evolved from dinosaurs.
Pick out a similar feature that is the product of convergent evolution and we will discuss. I promise that you will be very disappointed. Convergent features are only superficially similar. An examination of the specific features demonstrates that they were derived through different means.
Also, you first argue that we should see a nested hierarchy if creationism and baramins are true, and now you are arguing that there are clear violations of the nested hierarchy. It would be nice if you were more consistent.
As to birds and dinosaurs, birds are now classified as dinosaurs. The Aves clade sits within the theropod dinosaur clade along with such famous dinosaurs as raptors. Given the number of dinosaurs with feathers and the numerous transitionals between non-avian dinosaurs and birds the matter has been settled. Can you explain why there is not a baramin that contains mammals with bird features or birds with mammal features? Evolution can explain it.
1. As I've stated previously scientists must either accept intelligent design or abiogenesis (or some as yet unknown third method). Since many scientists can't get away from ID fast enough they make the assumption of abiogenesis. Admittedly, not all do - some are wise enough to realize just how foolish abiogensis is: there is no working theory as to how it could take place and a host of evidence against it as a possibility.
You don't have to assume either one in order to conclude that life has changed over time through the mechanisms of evolution and shares a universal common ancestor. Darwin himself suggested that life was breathed into a single mor many forms by a creator from which all life evolved.
2. Uniformation in the geological record is all well and good if the world were static - but it is not. Catastrophic events have been demonstrated to rapidly change geological formations (see creation research published RE: the Mt. Saint Helens eruption of 1980).
You just used uniformitarianism when you compared modern catastrophic events to evidence past catastrophic events. Of course catastrophic events are taken into account because we can observe them creating geologic structures today. These observations allow geologists to determine if a geologic structure was produced by gradual or catastrophic means. A good example is the Channeled Scablands in the northwestern United States which hold strong evidence for catstrophic formation, and geologists interpret it as such. We also have the chalk cliffs at Dover which can only form slowly over long spans of time due to the fact that they are formed from tiny creatures (coccolithophores) settling slowly to the ocean floor in calmer waters. You can't get chalk cliffs hundreds of feet high in a flood. Doesn't work that way.
3. You are correct that over the past century science has observed a fairly steady rate of radio-isotope decay. However, assuming that same constant rate of decay for 4+ billion years is a bad assumption. As it turns out radio-isotope half-lives can vary substantially based upon a host of factors.
This has been tested inside and out. The pressures and energies needed to change the half lives of the isotopes used for dating would destroy the rocks. We can also look at distant supernovae that are hundreds of thousands of light years away and observe the same decay rates. On top of that, we can also look at naturally occuring nuclear reacotrs (e.g. Oklo reactors) and observe the results of the same half lives. Read more here. In order to change the decay rates of isotopes in a way that would falsify an old earth would require scientific laws to be turned on their head.
You don't, of course. But I'm not referring to the supernatural as a testable hypothesis. I'm referring to it as a prior assumption in cases where no naturalistic assumption is reasonable.
If no naturalistic explanation is reasonable then you keep searching for one. That is how science works. Thousands of years ago there was no reasonable natural explanation for lightning so people ascribed it to the actions of the supernatural. How did that work out for them? What you are describing is a God of the Gaps, a deity who resides in our ignorance. As we learn more about nature your god gets smaller and smaller. Is that really the way you picture your god?
For baramins specifically, I know if know test capable of falsifying the hypothesis - just as there is none for common ancestry.
There are many ways to falsify common ancestry. A rabbit in pre-cambrian strata. A bird with three middle ear bones. A bird with teats. A bat with feathers. There are thousands and thousands of potential falsifications for common ancestry. So what evidence, if found, would falsify baramins? Nothing? Are you telling me that no matter what evidence I show you that it will never convince you that baramins are false?
The only way to test either hypothesis would be to re-run history which (at present) is impossible.
That is completely wrong. The theory of evolution makes millions of predictions about what one should and should not see in modern species, in fossil species, and in the genomes of modern species if evolution is true. I have listed a few above (e.g. bats with feathers). These predictions have been shown to be true for the last 150 years. Genetics was perhaps the biggest test for evolution in its history, and it passed with flying colors. Can you name a single prediction made by baraminology?
Genetics and morphology are simply indicators and provide no actual proof of common ancestry. If they did we wouldn't have any need for this conversation, would we? The only way to establish proof of common ancestry is to re-run history - still impossible since we last checked two paragraphs above.
The reason that we are having this conversation is that religious dogma has blinded you. Nothing more. Genetics and morphology are the evidence for common ancestry, evidence that your religious beliefs have blinded you to. We don't need to re-run history. We have that history. It is found in the fossil record and in the genomes of living species.

This message is a reply to:
 Message 143 by BobTHJ, posted 06-03-2010 7:26 PM BobTHJ has replied

Replies to this message:
 Message 198 by BobTHJ, posted 06-07-2010 3:26 AM Taq has replied

  
Taq
Member
Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


Message 149 of 385 (563339)
06-04-2010 12:01 PM
Reply to: Message 148 by Percy
06-04-2010 11:38 AM


You include a bunch of stuff about abiogenesis, geology and radiometric dating, but I won't address these parts since they're off-topic.
I second that motion. There are other threads for those topics. To BobTHJ, let's just focus on common ancestry, nested hierarchy, and baraminology.

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 Message 148 by Percy, posted 06-04-2010 11:38 AM Percy has seen this message but not replied

  
Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


(1)
Message 162 of 385 (563397)
06-04-2010 5:48 PM
Reply to: Message 156 by BobTHJ
06-04-2010 5:05 PM


Re: Getting down to details
No fossil in and of itself would falsify Baraminology - because baramins are based on the work of an omnipotent Creator, who could (theoretically) make anything he desired.
This would include feathered bats, would it not?
It could be falsified if clear evidence were shown for common ancestry between chimps and humans - but the evidence for this (at present) is far from conclusive.
What evidence would you accept for human/chimp common ancestry, outside of time travel? Any?
The fossil evidence clearly shows transitional fossils with a mixture of basal ape and modern human features.
The genomes of both humans and chimps carry irrefutable markers that point to common ancestry (e.g. shared pseudogenes, ERV's).
What more do you want?
The supposed age of the fossil is based on scientifically irresponsible dating techniques.
We don't even need radiometric dating to show evidence for evolution. Just the relative depth in the geologic column is enough, as is the mixture of characteristics in each fossil. We see the intermediate fossils that the theory of evolution says we should find (e.g. mammal-like reptiles, feathered dinosaurs, hominid transitionals) and none of the intermediates that we should not see (e.g. half mammal/half birds, half monkeys/half dogs). You yourself admit that a creator could create all types of intermediates, including those evolution says we should not find. How does this not indicate common ancestry and evolution?
You successfully list SOME assumptions - and I agree that these assumptions are made in most all cases, these are the common assumptions. Any conclusions based on evidence are assumptions as well. If new data or a more logical interpretation of the data comes to light then those conclusions can be shown to be false. I'm surprised you are having trouble seeing this.
Nope, those are the assumptions. I find it strange that you accuse me of not seeing these other assumptions and then fail to describe them yourself.
Phylogenetics is a useful tool ONLY if the assumption of common ancestry is correct.
Flatly wrong. It is useful period. Using an algorithm based on evolution scientists are capable of predicting the function of proteins with 96% accuracy.
quote:
PLoS Comput Biol. 2005 Oct;1(5):e45. Epub 2005 Oct 7.
Protein molecular function prediction by Bayesian phylogenomics.
Engelhardt BE, Jordan MI, Muratore KE, Brenner SE.
Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, United States of America. bee@cs.berkeley.edu
Abstract
We present a statistical graphical model to infer specific molecular function for unannotated protein sequences using homology. Based on phylogenomic principles, SIFTER (Statistical Inference of Function Through Evolutionary Relationships) accurately predicts molecular function for members of a protein family given a reconciled phylogeny and available function annotations, even when the data are sparse or noisy. Our method produced specific and consistent molecular function predictions across 100 Pfam families in comparison to the Gene Ontology annotation database, BLAST, GOtcha, and Orthostrapper. We performed a more detailed exploration of functional predictions on the adenosine-5'-monophosphate/adenosine deaminase family and the lactate/malate dehydrogenase family, in the former case comparing the predictions against a gold standard set of published functional characterizations. Given function annotations for 3% of the proteins in the deaminase family, SIFTER achieves 96% accuracy in predicting molecular function for experimentally characterized proteins as reported in the literature. The accuracy of SIFTER on this dataset is a significant improvement over other currently available methods such as BLAST (75%), GeneQuiz (64%), GOtcha (89%), and Orthostrapper (11%). We also experimentally characterized the adenosine deaminase from Plasmodium falciparum, confirming SIFTER's prediction. The results illustrate the predictive power of exploiting a statistical model of function evolution in phylogenomic problems. A software implementation of SIFTER is available from the authors. emphasis mine

Using the theory of evolution is more useful than just straight homology algorithms for predicting protein function. Can you show us anyone who is using an algorithm based on baraminology to predict protein function? No?

This message is a reply to:
 Message 156 by BobTHJ, posted 06-04-2010 5:05 PM BobTHJ has replied

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Taq
Member
Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


Message 206 of 385 (563972)
06-07-2010 2:32 PM
Reply to: Message 198 by BobTHJ
06-07-2010 3:26 AM


Order - order is an attribute of the Creator. Sorry for the confusing language.
What does "order" have to do with a nested hierarchy? Stars do not fall into a nested hierarchy, so were they not created by a Creator?
No, I did not argue for nested heirarchy.
Are you saying that we would not expect a nested hierarchy for separately created kinds?
The "dinosaurs are bird ancestors" debate certainly isn't closed among darwinists
Actually, yes it is. There are still some stubborn holdouts (e.g. Feducia), but the overwhelming scientific consensus is that modern birds are the descendants of theropod dinosaurs. Go to this tolweb page. They group birds WITHIN the dinosaur clade.
YEC can easily explain your question of why we don't see mammals with bird feathers: either the Creator chose not to make such creatures or they exist and we have not yet discovered them. I don't see how this is a problem?
That's not an explanation. That's a dodge.
""We do not know how this is, but we know that God can do it." You poor fools! God can make a cow out of a tree, but has He ever done so? Therefore show some reason why a thing is so, or cease to hold that it is so."--William of Conches
No, that still doesn't explain how life exists - and life must exist before darwinian evolution can run its course.
The germ theory of disease does not explain where the first germ came from. Does this mean we should throw out the idea that germs cause disease?
The theory of evolution explains how life has CHANGED over time. You don't need to know where life came from in order to know how it changed over time in the same way that you don't need to know where the first germ came from in order to know that tuberculosis is caused by an infectious bacteria.
No, I believe some things to actually have a supernatural explanation
People believe all sorts of crazy things. I'm not interested in beliefs. I am interested in what you can DEMONSTRATE THROUGH EVIDENCE. If you want to claim that something came about through supernatural means then DEMONSTRATE IT THROUGH EVIDENCE, not through the lack of evidence.
I'm telling you the only falsification test I can think of at the moment is evidence of a direct chimp/human common ancestry.
That's exactly what orthologous ERV's demonstrate:
"Given the size of vertebrate genomes (>1 109 bp) and the random nature of retroviral integration (22, 23), multiple integrations (and subsequent fixation) of ERV loci at precisely the same location are highly unlikely (24). Therefore, an ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place (14)."--Johnson and Coffin, 1999
Humans and chimps share thousands of orthologous ERV's. Consider kinds falsified.
I readily admit to a limited knowledge of baraminology. What's been discussed here so far is the full extent of my knowledge on the subject. To help answer you question I googled baraminology predictions and found this.
The first prediction is:
"The difference between two species in the same baramin would be mostly due to transposons."
How can you determine this without the ability to construct a baramin?
I find this to be entirely offensive. While I certainly hold strong religious beliefs (a fact I have not tried to hide) I make a good effort to evaluate the data for what it is.
No, you don't. You dismiss ERV's out of hand without even understanding how they operate, how they insert into the genome, or their impact on the host genome. You dismiss a nested hierarchy out of hand, as if common ancestry would not produce a nested hierarchy. You dismiss intermediate fossils. You misrepresent the scientific consensus on the ancestry of modern birds. You misrepresent what is and is not assumed in the science of radiometric dating. I will stop short of calling you a liar, but you have bought a bad bill of goods and the only reason I can think for why this is is due to your religious beliefs. Or do you really think that millions of highly trained physicists, geologists, and biologists wordwide from every culture and religion are wrong while a handful of religiously motivated creationists are right?

This message is a reply to:
 Message 198 by BobTHJ, posted 06-07-2010 3:26 AM BobTHJ has replied

Replies to this message:
 Message 259 by BobTHJ, posted 06-11-2010 5:23 PM Taq has replied

  
Taq
Member
Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


(1)
Message 226 of 385 (564155)
06-08-2010 4:21 PM
Reply to: Message 212 by BobTHJ
06-07-2010 5:54 PM


Re: Getting down to details
Yes, in a YEC model there could theoretically be a feathered bat.
So there is no mixture of characteristics, either in living or fossil species, that would falsify the YEC model? If not, then how do you explain the nested hierarchy? Other than evolution and common ancestry, what other mechanism would produce such a pattern of shared characteristics preferrentially over other patterns? Why do we see the exact pattern of shared characterstics that we would expect from evolutionary mechanisms if evolution never occurred? Is God trying to trick us into accepting evolution?
I'd like to dive into this topic a little deeper - and I fully admit I'm bumping into the limits of my knowledge on the subject. I'd like to learn more - and I'd be happy to let you guide me in that learning process if you wanted to set up a separate thread for such purpose. Though I admit - I'm starting to get spread a little thin here....I'm behind about 20 posts of replies at this point (and the OCD in me prevents me from just ignoring those replies).
You may want to check out this thread. I can understand that you are getting in over your head. If you want to discuss ERV's more you can either comment on the thread above or start a new one with questions not covered in the other thread.
My point is that initial conclusions are then used as assumptions for further evaluation of data.
The initial conclusions are based on the data. They are not assumed. There is no assumption in the chain at all. Or are you arguing that we need to know everything before we can know anything?
Take the example of radiometric dating - once a common decay rate is concluded - that conclusion is then assumed to be correct when evaluating the age of a fossil.
If the conclusion is based on mountains of solid data why shouldn't you conclude that decay rates are constant? Are you saying that we should ignore the data because you don't like the conclusion?
But if one (or more) of the base conclusions/assumptions turns out to be wrong all subsequent conclusions based upon that assumption must be re-evaluated
And until such time the conclusions are solid. To bring us back on topic, you need to explain why the non-avian dinosaur baramins are only found beneath rocks with isotope ratios consistent with 65 million years worth of decay. If both evolution and radiometric dating are wrong, how does this happen? How does YEC explain this? Even more, how does the YEC model explain how post-flood survival correlates with the depth of ancestral fossils? For example, we only find trilobites deep in the geologic record and there are no surviving trilobites. Rhinos are found much higher in the fossil record, and they survive today. How does the YEC model explain this? How does depth of burial affect post-flood survival with respect to baramins?
OK, you've got me interested - can you provide me with some links detailing further information on the SIFTER project? I'd like to learn more.
Full paper. Quick quote:
quote:
Phylogenomics is a methodology for annotating the specific molecular function of a protein using the evolutionary history of that protein as captured by a phylogenetic tree [17]. Phylogenomics has been used to assign precise functional annotations to proteins encoded in a number of recently sequenced genomes [27,28] and specific protein families [29], despite being a time-consuming manual process. Phylogenomic ideas have also proven helpful for addressing general evolutionary questions, such as showing that horizontal gene transfer is much less common between bacteria and human genes than was suggested in the original publication of the human genome [30,31].
Phylogenomics applies knowledge about how molecular function evolves to improve function prediction. Specifically, phylogenomics is based on the assertion that protein function evolves in parallel with sequence [32], implying that a phylogeny based on protein sequences accurately represents how molecular function evolved for that particular set of proteins. Additionally, molecular function tends to evolve more rapidly after duplication than after speciation because there are fewer mutational constraints; thus, mutations that alter function may more easily fixate in one of the copies [33—35]. These observations give rise to the phylogenomics method, which involves building a phylogenetic tree from homologous protein sequences, marking the location of duplication events, and propagating known functions within each clade descendant from a duplication event. This produces a set of function predictions supported by the evolutionary principles outlined above.
And what happens when you apply this evolution based algorithm? Very accurate protein function predictions. The theory works. Baraminology doesn't.
Edited by Taq, : No reason given.

This message is a reply to:
 Message 212 by BobTHJ, posted 06-07-2010 5:54 PM BobTHJ has replied

Replies to this message:
 Message 272 by BobTHJ, posted 06-12-2010 4:45 PM Taq has replied

  
Taq
Member
Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


(1)
Message 227 of 385 (564157)
06-08-2010 4:28 PM
Reply to: Message 224 by BobTHJ
06-08-2010 3:01 PM


Re: Getting down to details
Woods hypothesis is supported by the evidence. The fossils do separate into human and non-human - there were just two groups of non-humans. It may not be the conclusion you would come to as a darwinist - but it is the reasonable conclusion given a YEC model.
What features must a fossil have in order to be transitional between non-humans and humans in the YEC model? Or are such conclusions forbidden a priori? How can you claim to be reasonable if a specific conclusion is forbidden before even looking at the fossils?
I briefly reviewed these....and I've seen similar charts in the past. Creationists have a variety of evidential reasons to not accept many of the "hominid" fossils as human ancestors - but that seems to be beyond the scope of this thread.
I will fully agree that no fossil can be shown to be an ancestor of any living human. Only DNA can show this, and hominid fossils don't have DNA in them. However, if humans did evolve from a common ancestor with other apes shouldn't we see fossils with a mixture of basal ape and modern human features? We should, shouldn't we? Isn't that exactly what we see with these fossils? If apes and humans were created separately then why do we see fossils that have a mixture of human and ape features?
This is pure rubbish. You discredit Dr. Wile because he does not subscribe to a mainstream view on radiometric dating - a dissenting viewpoint does not indicate ineptitude.
Dr. Wile's explanations demonstrate his ineptitude.

This message is a reply to:
 Message 224 by BobTHJ, posted 06-08-2010 3:01 PM BobTHJ has replied

Replies to this message:
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Taq
Member
Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


Message 245 of 385 (564287)
06-09-2010 1:56 PM
Reply to: Message 232 by BobTHJ
06-08-2010 9:35 PM


But that is exactly what has happened. Mainstream atheistic scientists have ruled out an intelligent supernatural Creator as "unevidenced" and yet advanced abiogenesis through chemical evolution - a hypothesis with striking evidence against it. The only logical explanation for such behavior is a bias toward their atheistic darwinistic 'religious' dogma.
Since we know so little about how life could arise from non-living matter how could it be falsified? Right now, abiogenesis is in the discovery mode. They are trying to find the most plausible scenario, be it DNA first, RNA first, Protein first, or completely different chemistry such as PNA. It reminds me of what Lord Kelvin said in 1895, "Heavier than air flying craft are impossible".
And you are right. Scientists are biased. They are biased towards concepts that are evidenced and testable. How is that a bad thing? Also, how do you explain the fact that about 30% of biologists who accept evolution are also theists, not atheists. Are you saying that tens of thousands of christians are involved in a conspiracy to quash any scientific work related to a supernatural designer?

This message is a reply to:
 Message 232 by BobTHJ, posted 06-08-2010 9:35 PM BobTHJ has replied

Replies to this message:
 Message 286 by BobTHJ, posted 06-13-2010 3:48 AM Taq has not replied

  
Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


Message 262 of 385 (564688)
06-11-2010 6:28 PM
Reply to: Message 259 by BobTHJ
06-11-2010 5:23 PM


Baranomes are the set of genomes initially created by God - one for each created kind. Baranomes are incredibly vast - containing dormant material for a variety of variations. Baranomes contain VIGEs (Variation Indicuing Genetic Elements) - what mainstream biologists would call ERVs, transposons, etc. VIGEs modify the genome in an orderly fashion causing rapid adaptation and speciation among kinds. Over time however these VIGEs are disabled or repurposed by mutation leading to the variations of mobile DNA we see today. Some of these VIGEs have lost their controlling functions and now jump around haphazardly - modern retroviruses. Over time mutation and selective pressure eliminate function from the baranome among certain populations resulting in the modern genomes we see today.
ERVs similarities between humans and chimps don't post a problem in this hypothesis. Rather than being the result of a retroviral insertion they are instead remnants of VIGEs present in the baranome at creation. Since humans and primates share similar mophological features it logically follows that their initial baranomes would have had much similarity.
None of this explains why ERV's fall into a nested hierarchy. It also asserts that the retroviral function is recent without any supporting evidence. It is simply asserted. The fact of the matter is that ERV's can be pulled out of genomes and made into viable retroviruses:
quote:
Human Endogenous Retroviruses are expected to be the remnants of ancestral infections of primates by active retroviruses that have thereafter been transmitted in a Mendelian fashion. Here, we derived in silico the sequence of the putative ancestral progenitor element of one of the most recently amplified familythe HERV-K familyand constructed it. This element, Phoenix, produces viral particles that disclose all of the structural and functional properties of a bona-fide retrovirus, can infect mammalian, including human, cells, and integrate with the exact signature of the presently found endogenous HERV-K progeny. (source)
I have a good test for retroviral function. The long tandem repeats (LTR's) are genetic promoters found at each end of the viral genome (the 5' and 3' LTR's). In a functional retrovirus the 5' and 3' LTR's are identical at the time of insertion. As the ERV resides in the genome over several generations mutations will occur in each LTR resulting in the divergence of the LTR sequences. This offers an independent test of the common ancestry model that requires functional retroviral activity.
diagram:
5'LTR------viral genes (gag, pol, env)------3'LTR
So how do we test common ancestry using this information? Easy. The longer an ERV has been in a lineage the more divergent the LTR's will become. Therefore, an ERV shared by all apes will have more LTR divergence than an ERV shared by just humans and chimps. Guess what? This is exactly what we see in the genomes of apes.
quote:
Third, sequence divergence between the LTRs at the ends of a given provirus provides an important and unique source of phylogenetic information. The LTRs are created during reverse transcription to regenerate cis-acting elements required for integration and transcription. Because of the mechanism of reverse transcription, the two LTRs must be identical at the time of integration, even if they differed in the precursor provirus (Fig. ​(Fig.11A). Over time, they will diverge in sequence because of substitutions, insertions, and deletions acquired during cellular DNA replication. source
Here is an additional test for you. Let's say you do a PCR run and find that chimps and gorillas have ERV's from a specific retroviral family, but this same retrovirus is not found in humans and orangutans. Would you expect them to be in the same places in the genomes of gorillas and chimps based on baranomes?
Creation science (while no doubt a minority) is not the domain of extreme fringe.
You may want to rethink that.
There are many who scientists who believe in Biblical creation - for reference here's a list and here's another (neither are comprehensive, though there may be some overlap).
Just for giggles, how many are named Steve (or derivations thereof such as Estaban or Stephen)?
my only reason for believing the YEC model is because it's a better fit for the data I have reviewed.
The YEC model can not explain the nested hierarchy, ERV placement in the genome, LTR divergence in ERV's, intermediate fossils, the order of fossils in the geologic record, and just about everything else in the fields of geology and biology. Sorry, but I have a very hard time taking you seriously when you say things like this.
Edited by Taq, : No reason given.

This message is a reply to:
 Message 259 by BobTHJ, posted 06-11-2010 5:23 PM BobTHJ has replied

Replies to this message:
 Message 303 by BobTHJ, posted 06-14-2010 7:13 PM Taq has replied

  
Taq
Member
Posts: 9944
Joined: 03-06-2009
Member Rating: 4.9


Message 296 of 385 (565039)
06-14-2010 1:08 PM
Reply to: Message 272 by BobTHJ
06-12-2010 4:45 PM


Re: Getting down to details
Remember: nested hierarchy does not imply common ancestry. For example, I could build a nested hierarchy of automobiles. In one clade you'd have all the semi-tractors and in a distant clade on another branch you'd have the divergence between 2-door and 4-door sedans.
But that's just it. There is no single nested hierarchy for automobiles. You can have two Ford trucks, one with a Cummins deisel and the other with a Ford engine. You can have a Chevy and Ford with the same tires and the same airbags. Depending on what features you pick you will get a different nested hierarchy. This is not so with life. Life fits in a single nested hierarchy. There are no animals with teats and feathers, as one example.
This is the whole point I have been trying to get across. Things that are designed do not fall into a single nested hierarchy. Things that evolve do fall into a nested hierarchy. Life falls into a single nested hierarchy. How is this not indicative of common ancestry?
The YEC geological model has most sedimentary layers laid down during the global flood. It follows then that simple marine bottom-dwelling animals (such as trilobytes) would be found in the lowest pre-cambrian/cambrian strata as these would be the first to be buried. Larger and/or more advanced creatures would be buried later as they would be better equipped to survive against the rising waters and would survive longer. I'm not going to claim to be an expert on the fossil record according to YEC - so I doubt I can answer all your questions satisfactorily - but that is a synopsis.
This doesn't explain how flowering plants outran ferns. This doesn't explain the correlation between radiometric dating and the fossil species found. This explanation fails on every level.
It only makes sense then that by looking at proteins of closely grouped creatures you can predict the function of a similarly constructed protein for another creature within the group. This does not require common ancestry.
Without common ancestry there is no reason that separately created species would even share the same genetic molecule, much less the same genes.

This message is a reply to:
 Message 272 by BobTHJ, posted 06-12-2010 4:45 PM BobTHJ has replied

Replies to this message:
 Message 322 by BobTHJ, posted 06-16-2010 3:44 AM Taq has replied

  
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