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Creationist Inquiry

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Creationist Inquiry
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LaurensSocial EditorUser avatarPosts: 2950Joined: Sat Mar 20, 2010 11:24 pmLocation: Norwich UK Gender: Male

Post Re: Creationist Inquiry

Tsentralka wrote:P.S. Laurens, please read the opening post for the answer regarding microevolution. Furthermore, I am what you would call a YEC.


Okay, so you do not accept that the earth is billions of years old.

Now I am guessing you will dismiss radiometric dating that shows the actual age of the earth (otherwise you wouldn't call yourself a YEC). I'll ignore these for now, despite the fact that dismissal of radiometric dating does provide problems with the laws of physics themselves. Lets look at other reasons to believe that the earth is older than the YEC model. I'll keep these brief, but I shall provide links for further reading.

Dendrochronology

The counting of annual growth rings of tress is well known to show the age of trees. Some chronologies date over 9000 years into the past (see link for how chronologies are formulated).

Lake Suigetsu Algal Blooms

Each year there is an algal bloom in Lake Suigetsu, Japan. These algae die and then create a thin white layer on the bottom of the lake. For the rest of the year clay sediments build up on top of these, creating an alternating pattern of light and dark bands. Scientists have counted 45,000 layers dating back to around 43,000 BCE.

Greenland Ice Cores
Annual ice layers in the Greenland ice cores can be used to date back over 60,000 years.

Coral Reefs
The Eniwetok atoll coral reef is 4610 feet tall. The coral has been measured to grow at 5mm per year, this can be used to estimate that the Eniwetok atoll reef is 280,000 years old. "A similar analysis for the much larger Grand Bahama Reef reveals an age of 790,000 years."

Geomagnetic Reversal
We know the rate at which the width of Atlantic Ocean is increasing. Reversals in the earth's magnetic field are recorded along the floor of the Atlantic. These are recorded for the past 80 million years (see link for details).

Helioseismic Dating
Helioseismic dating shows that the sun is 4.57 billion years old. This agrees with the radiometric age of the solar system.

Finally take a look at this image:



You can see that the layers of sediment at the bottom of this outcrop are tilted diagonally. These sediments will have built up gradually over long time periods, and then would have been titled diagonally by geological forces. As you can see, another horizontal layer of sediment has built up on top of the diagonal layers. These kinds of geological processes take millions of years, no process can account for this occurring on a short timescale.

There are many, many other evidences for an old earth. All of them agree that the earth is older than a few thousand years. The only evidence for a young earth is that someone added up the genealogies in the Bible and came up with a date of roughly 6000 years - there is no other evidence to corroborate this, and no reason to assume that the genealogies in the Bible are accurate.

Given this evidence, and the evidence for microevolution, there is no reason to dismiss macroevolution, given that it is essentially the consequence of microevolutionary changes over vast geological time scales.
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Sat Feb 16, 2013 10:43 pm
InfernoContributorUser avatarPosts: 2298Joined: Thu Apr 30, 2009 7:36 pmLocation: Vienna, Austria Gender: Cake

Post Re: Creationist Inquiry

Tsentralka wrote:According to the Creation model


Which one? There are at least ten different ones. Are we talking about one of the three incompatible Hovind "theories"? Or the sometimes inconsistent one from AiG? Are you throwing stuff from Crone, Pendleton, Juby and Giglio into the mix? Or are you talking about ID, including BioLogos and that kinda stuff? Surely you don't accept Ross's model, he's an old earth creationist. Also surely not Harun Yahya's model, he's a Muslim creationist.

Which one is it? Which one isn't it?
BTW, don't answer, the above is a series of rhetorical questions.

Tsentralka wrote:We all agree that Guinea pigs, bats, and humans all lost their GULO functionality independently...this is not what is in question.


Agreed.

Tsentralka wrote:According to the Creation model, humans and chimps must also have lost GULO functionality independently, IOW the human and chimp sequences each represent different wrong answers. I assume that one of those references from Jerry Coyne address this specifically. Inferno can you sum up in a sentence or two what we should find if the loss of GULO in chimps and humans represent a single event?


I thought I did, but I'll try to make myself clear.
Falseorigins will help me make my point clear:
Their excellent two pictures
http://i819.photobucket.com/albums/zz112/Infy_2010/Creo_zps9f6a2282.jpg
demonstrate one thing quite clearly: If chimps, humans and pigs all lost their GULO independently, then we'd expect them to be different in the same way. Or in other words, we'd expect humans to have a mutation at location A, chimps a mutation at location C and pigs a mutation at location E.
If we were to compare them to a functioning version of the GULO, we'd expect them all to have mutated at about the same pace (or distance), but in different directions.

For the creation model, we'd expect something like the following:

Imagine that the following string of ACGT letters represents a functioning GULO, a human, a chimp and a pig inactivated version. (Note: They're gibberish, I'm just trying to make a point.)
Functioning: ACGTACGTACGTACGTAG
Human: ACGTAAAAAAAAACGTAG
Chimp: ACGTCCCCCCCCACGTAG
Pig: ACGTTTTTTTTTACGTAG

They're all 18 letters (or six triplets) long, all have six mutations and all are equally different from one another.

Now if, on the other hand, evolution were true, we'd expect something similar to the below:
Functioning: ACGTACGTACGTACGTAG
Human: ACGTAAAAAAAAACGTAG
Chimp: ACGTAAAAGAAAACGTAG
Pig: ACGTTTTTTTTTACGTAG

Now as you can see, they still all have 18 letters, they all have six mutations, but the Chimp and Human sequence are very close together. I could calculate the likelihood of that particular sequence being that similar, but the real sequence is about 300 letters long, so you'd have to make a new calculation for that.

Now in the first picture (Table 1 from Source 3: Random nucleotide substitutions in primate nonfunctional gene for L-gulono-γ-lactone oxidase, the missing enzyme in L-ascorbic acid biosynthesis) I posted, we see exactly that:
Human and chimp sequences being very similar, Human and Orangutan sequences being slightly less similar and Human and Macaque sequences being the least similar of them all. And Chimps and Orangutans are more similar to each other than Chimp and Macaque.

Source 1 gives you a direct comparison between the Rat and Human GULO sequences, so you can compare that to Source 3, Source 4 compares the Rat and Guinea Pig sequences and Source 2 has a slightly more updated version of Source 1's Human sequence.

I won't hold it against you if you would like to go through every single letter and compare which ones are more similar, but the conclusion is the one given in the four papers, which I've summarized above:
Humans, pigs and bats lost their GULO-genes independently of each other, but Humans and Chimps share a gene-loss-event, which happened roughly 35-65 mya.

Tsentralka wrote:An important aspect of the Creation model is that genetic similarity is explained largely by anatomical/physiological similarity. As Aught3 mentions, if you grouped organisms based on morphological similarities to produce one nested hierarchy and then grouped organisms based on the similarity of their protein coding genes it would yield the same nested hierarchy (I assume)...twin-nested hierarchy. However, I would argue that this is due to the genotype-phenotype correlation (phenotype here not referring simply to morphology). In this model, DNA which does not contribute to the anatomy/physiology of an organism (functionless DNA) should not produce a nested hierarchy which matches one which groups organisms based on anatomy/physiology. This is what I tried convey in the first post (and based on Aught3's post I think some people got it), but I should have made it more clear.


Thanks for clearing that up.
However, I already showed this to be wrong when I pointed to Thylacines and Wolves. They're very similar to each other, but their DNA-sequences are not as closely matched as, say, the Wolf and the German Shepherd or the Boxer. And remember that Thylacines and Wolves are morphologically so similar that biology students are habitually asked to tell them apart and are failed on their exam if they can't do that.
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Sun Feb 17, 2013 12:09 am
he_who_is_nobodyBloggerUser avatar
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Post Re: Creationist Inquiry

Tsentralka wrote:
Inferno wrote:Give us some indication of what we should find to falsify your (the creationist) hypothesis.

…here is potential falsifying evidence from comparative genetics. 1) Non-functional DNA sequences should NOT be able to group organisms into a twin nested hierarchy. Or to phrase this in a positive light, every DNA sequence which forms a twin-nested hierarchy should have a functional significance.


In this paper, scientists were able to use non-coding DNA to create a twin-nested hierarchy with other coding DNA sequences, thus, falsifying creationism according to you.

Tsentralka wrote:2) Multiple shared, random mutations should NOT exist between different Kinds of organisms. I consider humans and chimps to be different Kinds, so there should no random mutations in humans which also exist in chimps (and vice versa) except for few expected from random chance.


Besides GULO, which has been covered quite well, in how it also falsifies creationism, I submit vestigial ear muscles found in all hominids. The reduction in size found in all apes (apes include humans by definition) compared to its basal form seen in most other primate species is an example of a shared random mutation, thus also falsifying creationism according to you.

Have a nice day. :)
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Sun Feb 17, 2013 3:21 am
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RumraketUser avatarPosts: 1170Joined: Fri Jun 25, 2010 7:49 am Gender: Male

Post Re: Creationist Inquiry

Hello Tsentralka and welcome to the forum.

If you really want to see the evidence from phylogenetics(whether ERV's, pseudogenes or just protein-coding etc.) try this webpage out:
http://www.evolutionarymodel.com/

Read it all, go through each single subject and digest it one by one.

The thing about phylogenetics is creationists, at least the dishonest ones among them, will usually pick out minor deviations and keep referring to them as if they constitute a falsification of the main pattern. In doing so, they neglect to mention that the evidence for common ancestry in the nested hierarchies from comparative phylogenetics are not resting on a single or few ERV's or pseudogenes, like GULOP or whatever couple of ERV's are occasionally found that don't fit. What is actually the case is that there are hundres, sometimes thousands of pseudogenes and ERV's that fall within the expected nested hierarchy, and actually only very few exceptions to the pattern. This is actually expected from the evolutionary model, because evolution is largely stochastic you'll get occasional deviations from the main pattern through mechanisms like genetic drift, and incomplete lineage sorting etc. Also, it's not just ERV's and pseudogenes that form the nested hierarchy, almost all genes or loci, whether non-coding regulatory sequence, protein-coding regions or just plain non-functional DNA that mutates at a neutral rate, most of it will fit the nested hierarchy.

What this means is that the evidence for evolution is not all or nothing, it's probabilistic. If we are related through common descent, the main pattern of a nested hierarchy should overshadow the deviations the more closely related we are. This is true both in terms of the degree to which similar sequences diverge, but also in the number of genes shared. Closer related species will share more genes, and their genes will show greater degree of similarity. But there will always be deviations, but the interesting thing to note when you think about it is that even the dissimilarities should show their own special pattern. The more distantly related we are, the more dissimilar in sequences and the more genes we would expect to not be shared.

Another really good webpage dedicated to explaining these mechanisms is this:
http://biologos.org/blog/understanding-evolution-speciation-and-incomplete-lineage-sorting

Now you might ask if the evidence for evolution from comparative phylogenetics is really probabilistic at bottom, how can it be falsified?
The answer is that it's a matter of degree of course. If the situation with similarity vs dissimilarity was reversed, and instead of the main pattern being a nice nested hierarchy, but instead a scrambled mess, with only very very few similarities and an extremely weak and/or improbable hierarchy, then it would be strange to posit they evolved through common ancestry when there's so much evidence that just doesn't fit. (But again, the real situation is in fact the direct opposite).
"Nullius in verba" - Take nobody's word for it. https://en.wikipedia.org/wiki/Nullius_in_verba
Extraordinary claims require extraordinary evidence.
Sun Feb 24, 2013 8:32 am
TsentralkaUser avatarPosts: 9Joined: Wed Feb 06, 2013 11:41 pm

Post Re: Creationist Inquiry

Rumraket’s link to http://www.evolutionarymodel.com/ contained what I thought to be an excellent presentation of the GULO evidence. It appears to also reflect what has been argued here on this thread. The “facts” presented so far are: (quotes from evolutionmodel.com)

1. Strepsirrhines and most other plants and animals have the GULO gene, and are immune to deadly vitamin C deficiency (scurvy).
IOW, most mammals (including lemurs) have the ability to synthesize vitamin C due to the presence of the gene GULO.


Agreed…no issues here…(except that the claim that plants use the same gene/enzyme sounds a little fantastic…I doubt that’s true)

2. Haplorrhines (Inai, Ohta, & Nishikimi, 2003), the remaining primates, along with pigs (Hasan et. al., 1999), guinea pigs (Nishikimi, Kawai, & Yagi, 1992), and certain fish and birds are prone to vitamin C deficiency. Additionally, they posses an altered, inactive form of the GULO gene, as well as the genes for all the remaining enzymes in the metabolic pathway, such as UDP-glucose dehydrogenase (4p15.1) and glucuronic acid epimerase (15q23).


Agreed…no issues here…

3. Haplorrhine GULO inactivation is likely due to a missing base pair in the amino acid coding region of exon 10, which shifts its reading frame. This shift forms a stop codon several base pairs downstream of the missing base pair. Not only is this stop codon present, and is this base pair missing in all haplorrhine GULOs, but it is not found in the guinea pig GULO; which is likely inactivate due to one of 3 stop codons in exons 2, 3, and 6.


This is really the crux of the matter and it is where issues begin to arise. I say that the GULO gene was psuedogenized independently in both humans and the haplorrhines; whereas, Evolutionists would say they represent the same event. It is true that haplorrhines and humans share a deletion of one nucleotide in exon 10, but nobody claims that this was the initial mutation that caused the loss…or at least the researchers who found it didn’t claim this. Ohta et al 1999 is probably where they get this idea …nucleotide 97 is missing in both humans and the haplorrhines which, if the gene were active, would have resulted in a premature stop codon.

Ohta et al 1999 wrote:...in relation to this point [that GULO is a nonfunctional pseudogene], it should be emphasized that all of the primate species examined had a single nucleotide deletion at position 79 which causes a frameshift. These findings indicate again that the mutations in the primate GLO genes occurred without functional restriction after the loss of its function.


Image

https://www.dropbox.com/s/iq5c2lkp4w2ne3g/Ohta%20et%20al%20Exon%2010%20Sequence%20Alignment.jpg


Furthermore, an excellent recent review paper, Drouin et al 2011, states, “The nature of the initial mutations which inactivated the anthropoid primate and guinea pig GLO genes is not known.” So bottom line, this crucial point—that humans and apes share the same mutation which deactivated GULO—does not have scientific support. I don’t criticize you for believing that they were deactivated by the same mutation…if I were an Evolutionist, I would also believe that. You cannot, however, claim there is scientific evidence to support this directly.

4. There are many single nucleotide polymorphisms (SNPs) shared among haplorrhine GULOs, but not shared with the guinea pig GULO. And the shared haplorrhine SNPs fall in a hierarchical grouping, where each set falls within another set (a nested hierarchy).


Part 1 here is true…I have no issues. Part 2 (“And the shared…”) requires a good deal of looking into and will be dealt with in a bit.

The real argument lies in the interpretation of the data, yet before we even get to the interpretation, numerous problems have been found with the so-called data itself (namely Fact #3 above). Furthermore, it is evident based on posts in this thread that some of you have accepted these inaccuracies as the foundation for your belief in why the GULO pseudogene is evidence for common descent. I remind you again of the quote:

Drouin et al 2011 wrote:The nature of the initial mutations which inactivated the anthropoid primate and guinea pig GLO genes is not known.


Here is another excerpt from evolutionmodel.com.

Image

https://www.dropbox.com/s/tm7ssodg5sg2e91/EvolutionModel.com%20Comparison%20Table.jpg


First the Creationist perspective (right column)…

Point 1 is ridiculous…I’ve never heard a Creationist assume this. As you all know from previous posts, I believe humans, haplorrhines, guinea pigs, etc., each originally did have the ability to synthesize vitamin C but it was lost independently in each group (as we see happening before our eyes in vertebrates today, i.e. bats, pigs).

Point 2.1…I agree with the deactivating mutations part. Points 2.2-3 are both based on the inaccuracy of Fact #3 laid out at the beginning.

Now the Evolutionist perspective (left column)…

Point 1 is reasonable…that’s also what the Creationist position is.

Point 2.1 is reasonable…that’s also what the Creationist position is. Points 2.2-3 are both based on the inaccuracy of Fact #3 laid out at the beginning. So a lot is hanging on the inaccuracy of Fact #3. I’ve contacted the EvolutionModel.com administrator to note this error.

And then comes point number 3.

EvolutionModel.com wrote: Since pseudogenes accumulate mutations from generation to generation, and since the haplorrhine GULOP would have to have been in pseudogene form across many speciation events (and in turn, many common ancestors), we should find shared mutations (again, manifesting as shared SNPs), and we should find that they are arranged in such a way that they give an unbroken line of inheritance for every species (a nested hierarchy).


At this point it dawned on me…we are dealing with a two headed monster. The GULO pseudogene was brought up because the infamous deactivating mutation was supposedly shared between haplorrhines…this is the first head. The second head is a separate issue altogether, it is the issue of genetic homology…human DNA is similar to chimp DNA, slightly less similar to gorilla DNA, slightly less similar to orangutan DNA, etc. The switch from head number 1 (shared mistake) to head number 2 (shared SNPs) can be seen in this statement from Inferno:

Inferno wrote:You're confusing all students making a mistake on the same answer (what you detailed above) with all students making the same mistake on the same answers (what I will explain just now). [this is the shared mistake...Head #1]

Various animals losing the enzyme wouldn't be evidence, but what if the guinea pigs, birds, bats and pigs all had different sequences from the primate sequences?[this is the shared SNPs...Head #2]


That same switch from shared mistake to shared SNPs occurred in Fact #4 on the EvolutionModel.com and again in Point 3 of the comparison table. This is NOT a criticism…merely a clarification; both heads of this issue are valid points, but I think it better to disentangle them. Anyways, the whole point of this post is to present my thoughts about the shared mistake argument (the first head of the beast). I have presented evidence that we do not know that humans and other haplorrhines shared a deactivating mutation and that arguments which claim they do are based on misinformation. We cannot rule out the possibility that a common mutation deactivated the ancestral form, but the point is that we have no evidence to make this claim…the mutation was more than likely lost along with the other 9 GULO exons.

I am still considering head number two and will share what I come up with in a subsequent post. Along these lines I wanted to ask a few questions. The evidence presented by Inferno and EvolutionModel.com supporting that more closely related species have more SNPs in common is from the Ohta et al paper which describes nucleotide substitutions in exon 10 (first figure in post). Of course, a substitution is always relative to something (an ancestral sequence in the Evolutionist’s case). Why do you suppose they chose to use the rat GULO exon 10 sequence as the reference? How do we know that the rat sequence has not changed relative to the primate sequence?

Tsentralka

Addendum #1 – Thylacines and Wolves
Inferno are you suggesting that before the advent of molecular genetics, Thylacines was classified with canids? Keep in mind I’m not saying that college undergrads who crammed the night before for an exam should be the ones responsible for constructing these phenotypic based taxonomic groupings.

Addendum #2 – Age of the Earth
Laurens…I’m not going to lie, I did not read your most recent post. Criticize this is you must, but you can’t seriously expect me follow you down your bottomless rabbit trail. I realize that your belief in common descent necessitates your adherence to an old earth, but if your best evidence for common descent is an old earth, then we have some real issues.

Addendom #3 – Rumraket
I basically agree with your post regarding the nature of the evidence in support for common descent. If I find some out of place ERV or inconsistency I don’t expect it to dent your faith in Evolution. It is a matter of the volume of evidence. However, if I believed everything I heard from Evolutionists, I would be an Evolutionist. I’ve been around the block a few times and I have come to realize that people are prone to misrepresent evidence to support something they feel strongly about (both Evolutionists and Creationists). Your link to EvolutionModel.com is a perfect example. If I had taken their word for everything they said regarding GULO, then I might believe in common descent. Upon looking into it you find several important errors. You apparently did take their word for it and have gone on to propagate those errors (an honest mistake). So forgive me if I am skeptical when you say, “What is actually the case is that there are hundres, sometimes thousands of pseudogenes and ERV's that fall within the expected nested hierarchy, and actually only very few exceptions to the pattern.” We obviously don’t have time to look at all of these, so I am happy to just look at the best representative cases.



References:

Drouin et al 2011 The Genetics of Vitamin C Loss in Vertebrates
Ohta et al 1999 Random nucleotide substitutions in primate nonfunctional gene for L-gulono-γ-lactone oxidase, the missing enzyme in L-ascorbic acid biosynthesis

Note: Throughout this post and others, when I use capital “E”-Evolution (Evolution, Evolved, Evolutionist), I am referring to the colloquial (and very inaccurate) use of the term which encompasses the origin of the universe, the origin of life from non-living matter, and the development of that life over time into all life forms we see today; basically the naturalistic view of life and the universe (which I personally reject). When I use little “e”-evolution, I am referring to the more scientific definition, a change in genomes over time, or, more technically, a change in the distribution of alleles over generations.
Fri Mar 08, 2013 2:20 pm
he_who_is_nobodyBloggerUser avatar
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Post Re: Creationist Inquiry

Tsentralka wrote:Note: Throughout this post and others, when I use capital “E”-Evolution (Evolution, Evolved, Evolutionist), I am referring to the colloquial (and very inaccurate) use of the term which encompasses the origin of the universe, the origin of life from non-living matter, and the development of that life over time into all life forms we see today; basically the naturalistic view of life and the universe (which I personally reject). When I use little “e”-evolution, I am referring to the more scientific definition, a change in genomes over time, or, more technically, a change in the distribution of alleles over generations.


:|

he_who_is_nobody wrote:I am going to have to disagree with you right here. You have already admitted that this is an inaccurate use of the term so you might as well use the correct terms. When talking about the origin of the universe, it would be better to state big bang, when talking about the origin of life, it would be better to say abiogenesis, and when talking about development of life over time into all life, it would be better to say universal common descent. I suggest this, so right from the beginning we are not confusing terminology and arguing semantics down the line. Being clearer from the beginning will make this discussion flow so much smoother.
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Fri Mar 08, 2013 6:25 pm
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InfernoContributorUser avatarPosts: 2298Joined: Thu Apr 30, 2009 7:36 pmLocation: Vienna, Austria Gender: Cake

Post Re: Creationist Inquiry

Good to see you back, Tsentralka.

Tsentralka wrote:The “facts” presented


Why does this make me cringe?

Tsentralka wrote:This is really the crux of the matter and it is where issues begin to arise. I say that the GULO gene was psuedogenized independently in both humans and the haplorrhines; whereas, Evolutionists would say they represent the same event. It is true that haplorrhines and humans share a deletion of one nucleotide in exon 10, but nobody claims that this was the initial mutation that caused the loss…or at least the researchers who found it didn’t claim this. Ohta et al 1999 is probably where they get this idea …nucleotide 97 is missing in both humans and the haplorrhines which, if the gene were active, would have resulted in a premature stop codon.


Pseudogenized? I'd call it "deactivated", but whatever.
I'll get to your point in the second quote.

Tsentralka wrote:Furthermore, an excellent recent review paper, Drouin et al 2011, states, “The nature of the initial mutations which inactivated the anthropoid primate and guinea pig GLO genes is not known.” So bottom line, this crucial point—that humans and apes share the same mutation which deactivated GULO—does not have scientific support. I don’t criticize you for believing that they were deactivated by the same mutation…if I were an Evolutionist, I would also believe that. You cannot, however, claim there is scientific evidence to support this directly.


Stop! Read the paper again. (I have it in front of me.)
Drouin et al. do state what you said (“The nature of the initial mutations which inactivated the anthropoid primate and guinea pig GLO genes is not known.”), but it has nothing to do with what you say. I've underlined the relevant words: The nature ...
They don't know what sort of mutation it was (i.e. point mutation, insertion, deletion... that kinda thing) but they state quite frankly:
"Phylogenetic distribution of the ability to synthesize vitamin C in mammals."
Image

Heck, the paragraph you cite goes on to say:
The nature of the initial mutations which inactivated the
anthropoid primate and guinea pig GLO genes is not known.
The fact that exons are missing in both cases, together with
the observation that repetitive elements are often involved in
exon loss events [35], suggest that recombination between
repetitive elements could have been involved. However,
studies which investigated this possibility concluded that
such events were unlikely to have been involved in the inactivation
of the anthropoid primate and guinea pig GLO genes
[28, 36].


So again, they're unsure about the mechanisms, not the result. (Which is what you object to! Quoting their paper to do so is... interesting.)

As for your above point, that the "idea probably came from Ohta et al.":
Nobody, that is to say not Ohta et al. nor Drouin et al. state what you claim they do, at least not as far as I can see. Do you know why? Because that would be pointless speculation. They do however state that the mutations have occurred (which being the first, what the mechanisms were, which caused what... being up for debate, that's not addressed) and because of the evidence we have on the mutations (time stamps, orthologues, etc.) we can conclude the cladogram shown above.

I'll be even more clear.
Your statement
Tsentralka wrote:So bottom line, this crucial point—that humans and apes share the same mutation which deactivated GULO—does not have scientific support.

is simply not true. I showed that here and here, when I pointed out that bats, birds, pigs, guinea pigs and humans lost their genes independently (which you agreed with) and (in the second post) when I showed that humans and other primates did NOT lose it independently; we lost it together.

GULO loss shows exactly the traits we would expect if this trait were evolved and is consequently the exact opposite of what we'd expect if all "kinds" were specially created. I'd gladly argue that with you, but you jumped the gun and declared the very thing we're arguing to be false because... [insert absolutely no reason here].

Tsentralka wrote:The real argument lies in the interpretation of the data, yet before we even get to the interpretation, numerous problems have been found with the so-called data itself (namely Fact #3 above). Furthermore, it is evident based on posts in this thread that some of you have accepted these inaccuracies as the foundation for your belief in why the GULO pseudogene is evidence for common descent. I remind you again of the quote:


Apart from your misunderstanding of what Drouin said, aka. your false "Fact #3" problem, you're making another typical creationist mistake:
Image

But that's not how science works! Science works by questioning the assumptions and trying to disprove them at every turn, while the creationist position is one of "making the evidence fit with a sledgehammer".
That point is brilliantly made in the 3rd FFoC (everything's relevant, the punchline comes near 9:30), in FFoC 15 Part 1 and Part 2 as well as a myriad of posts online.

What you're suggesting, in effect, is that we all have an inherent bias, that we have a conclusion and then interpret the evidence according to our belief. But that's not true as you well know, so why are you trying to make that point?

Tsentralka wrote:I have presented evidence that we do not know that humans and other haplorrhines shared a deactivating mutation and that arguments which claim they do are based on misinformation. We cannot rule out the possibility that a common mutation deactivated the ancestral form, but the point is that we have no evidence to make this claim…the mutation was more than likely lost along with the other 9 GULO exons.


No, you didn't. What you showed us is that you misread something that has nothing to do with the issue at hand, ignored evidence contrary to your position from the very same post and apparently did not deign my posts worthy of scrutiny, even though I showed your point to be wrong before you even made it.
Go back and check, I've linked to all the necessary parts and I've even re-clarified the important bits again. If anything is unclear, feel free to ask but please, don't claim something which I can show to be in error simply by reading the very quote you offered.

Tsentralka wrote:The evidence presented by Inferno and EvolutionModel.com supporting that more closely related species have more SNPs in common is from the Ohta et al paper which describes nucleotide substitutions in exon 10 (first figure in post). Of course, a substitution is always relative to something (an ancestral sequence in the Evolutionist’s case). Why do you suppose they chose to use the rat GULO exon 10 sequence as the reference? How do we know that the rat sequence has not changed relative to the primate sequence?


Two reasons:
1) Because rats are more distantly related to primates than primates to each other and because the rat sequence is likely more primitive. But that's what we're trying to check here...
2) Because it had to be relative to something. Even if you had switched them around (compare all others to the human sequence) the results would be the same: All primate sequences are more closely related to each other than to the rat sequence, the human sequence is more closely related to the chimp sequence than to the macaque or orangutan sequence and so on. None of that is changed by comparing it to any other sequence.

Tsentralka wrote:Addendum #1 – Thylacines and Wolves
Inferno are you suggesting that before the advent of molecular genetics, Thylacines was classified with canids? Keep in mind I’m not saying that college undergrads who crammed the night before for an exam should be the ones responsible for constructing these phenotypic based taxonomic groupings.


While that might have been the case once, that's not at all my point. My point was that this sentence "An important aspect of the Creation model is that genetic similarity is explained largely by anatomical/physiological similarity." is blatantly wrong.
Genetically similar animals (various breeds of dogs) can have vastly different anatomy, while anatomically similar animals (wolves and thylacines) can have a completely different genetic make-up. In fact, that's the very mistake pointed out almost exactly five years ago, talking about Harun Yahya that time. And another time in July of the same year.
That's what you call convergence.

Tsentralka wrote:I basically agree with your post regarding the nature of the evidence in support for common descent. If I find some out of place ERV or inconsistency I don’t expect it to dent your faith in Evolution. It is a matter of the volume of evidence. However, if I believed everything I heard from Evolutionists, I would be an Evolutionist. I’ve been around the block a few times and I have come to realize that people are prone to misrepresent evidence to support something they feel strongly about (both Evolutionists and Creationists). Your link to EvolutionModel.com is a perfect example. If I had taken their word for everything they said regarding GULO, then I might believe in common descent. Upon looking into it you find several important errors. You apparently did take their word for it and have gone on to propagate those errors (an honest mistake). So forgive me if I am skeptical when you say, “What is actually the case is that there are hundres, sometimes thousands of pseudogenes and ERV's that fall within the expected nested hierarchy, and actually only very few exceptions to the pattern.” We obviously don’t have time to look at all of these, so I am happy to just look at the best representative cases.


This, I'm sorry to say, is a highly dishonest paragraph. Aside from the fact that the errors you noted weren't errors to begin with but misunderstandings on your part, you would at least regard the evolutionary model as internally consistent, otherwise you wouldn't say something like "if I believed everything I heard from Evolutionists, I would be an Evolutionist". Contrary, if I believed everything creationists told me, I would maybe not accept evolution, but I would certainly not accept creationism. As I already pointed out:

Which one? There are at least ten different ones. Are we talking about one of the three incompatible Hovind "theories"? Or the sometimes inconsistent one from AiG? Are you throwing stuff from Crone, Pendleton, Juby and Giglio into the mix? Or are you talking about ID, including BioLogos and that kinda stuff? Surely you don't accept Ross's model, he's an old earth creationist. Also surely not Harun Yahya's model, he's a Muslim creationist.

Which one is it? Which one isn't it?


Most of their ideas, and they're really nothing more than ideas, are mutually exclusive, internally inconsistent, highly absurd and inconsistent with the evidence. Maybe you could explain that in a different thread: Which model of creationism do you accept? Why? Why that one and not one of the others?
"Sometimes people don't want to hear the truth because they don't want their illusions destroyed." ― Friedrich Nietzsche

"I shall achieve my objectives through the power... of Science!" --LessWrong
Fri Mar 08, 2013 7:05 pm
RumraketUser avatarPosts: 1170Joined: Fri Jun 25, 2010 7:49 am Gender: Male

Post Re: Creationist Inquiry

Tsentralka wrote:Rumraket’s link to http://www.evolutionarymodel.com/ contained what I thought to be an excellent presentation of the GULO evidence. It appears to also reflect what has been argued here on this thread. The “facts” presented so far are: (quotes from evolutionmodel.com)

1. Strepsirrhines and most other plants and animals have the GULO gene, and are immune to deadly vitamin C deficiency (scurvy).
IOW, most mammals (including lemurs) have the ability to synthesize vitamin C due to the presence of the gene GULO.


Agreed…no issues here…(except that the claim that plants use the same gene/enzyme sounds a little fantastic…I doubt that’s true)

Well, it is. The gene has been found and sequenced in plants too and the protein enzyme purified from them. Here's some evidence:
http://www.ncbi.nlm.nih.gov/pubmed/10050319

Tsentralka wrote:
3. Haplorrhine GULO inactivation is likely due to a missing base pair in the amino acid coding region of exon 10, which shifts its reading frame. This shift forms a stop codon several base pairs downstream of the missing base pair. Not only is this stop codon present, and is this base pair missing in all haplorrhine GULOs, but it is not found in the guinea pig GULO; which is likely inactivate due to one of 3 stop codons in exons 2, 3, and 6.


This is really the crux of the matter and it is where issues begin to arise. I say that the GULO gene was psuedogenized independently in both humans and the haplorrhines; whereas, Evolutionists would say they represent the same event.

Yes, on matters of statistical likelyhood. It is MORE likely, on the order of millions of times more likely, that a deactivating mutation happened once initially and was subsequently inherited(after which the gene ackquired additional subsequent mutations independently in all lineages affected), than it is it happened independently multiple times in exactly the same way, in the same location, in the same exon.

Remember, the evidence for evolution from comparative phylogenetics is statistical in nature. It is probabilistic. It does not constitute a direct logical refutation of the hypothesis of independent origins, it's just that the evolutionary account is the simplest, most likely explanation for the evidence.
Ask yourself, what is the odds that in 5 or 10 or 20 different species, the same mutation(single nucleotide deletion) would happen in the same gene(GULOP) in the same exon(10), at the same postion(79), out of the total genome of these organisms, which is in the billions of basepairs?

Astronomical, unfathomable. Evolution wins in terms of likelyhood to an incomprehensible degree.

Yes, it's logically possible to explain the observation by postulating this mutation happened independently in all these species. But compared to the evolutionary account, it's much, much, much less likely. And there's really no good reason to retreat to such a postulate, which is entirely ad-hoc and doesn't follow logically from anything.

Tsentralka wrote: It is true that haplorrhines and humans share a deletion of one nucleotide in exon 10, but nobody claims that this was the initial mutation that caused the loss…or at least the researchers who found it didn’t claim this. Ohta et al 1999 is probably where they get this idea …nucleotide 97 is missing in both humans and the haplorrhines which, if the gene were active, would have resulted in a premature stop codon.

They don't have to explicitly state as much in the paper discovering the mutation, it's okay for other people to come back to the data and analyze it with intention of trying to explain the observation. Again, since the postulate that the mutation happened once and then got inherited is more likely, which is why it's tracing back to the beginning as the initial dactivating mutation also is the most likely.

It's not really an overly important point whether the mutation in question really was the initially deactivating mutation. The crucial matter is that it constitutes a deactivating mutation, and that it is shared between the different species. We're back to the statistical likelyhood of the number of shared mutations happening once and getting inherited, versus them all happening independently. This frameshift causing one is an obbvious candidate for being the cause of the initial loss, due to the fact that it's one of the ones being shared across the board in haplorrhines and resulting in a stopcodon due to it being a frameshift mutation.


Tsentralka wrote:
Ohta et al 1999 wrote:...in relation to this point [that GULO is a nonfunctional pseudogene], it should be emphasized that all of the primate species examined had a single nucleotide deletion at position 79 which causes a frameshift. These findings indicate again that the mutations in the primate GLO genes occurred without functional restriction after the loss of its function.


Image

https://www.dropbox.com/s/iq5c2lkp4w2ne3g/Ohta%20et%20al%20Exon%2010%20Sequence%20Alignment.jpg


Furthermore, an excellent recent review paper, Drouin et al 2011, states, “The nature of the initial mutations which inactivated the anthropoid primate and guinea pig GLO genes is not known.” So bottom line, this crucial point—that humans and apes share the same mutation which deactivated GULO—does not have scientific support.

You're focusing on the wrong piece of the claim. Whether the frameshift mutation really was the one that happened first isn't the important part, as I said it's merely a likely candidate due to the highly deleterios(to the gene) nature of the mutation and the fact that it's shared universally across haplorrhines.

The crucial matter is that it's shared(and it isn't the only one) and that, regardless of what other mutation exist in the gene, this one would in fact result in gene inactivation due to premature stop codon.

Tsentralka wrote:I don’t criticize you for believing that they were deactivated by the same mutation…if I were an Evolutionist, I would also believe that. You cannot, however, claim there is scientific evidence to support this directly.

I don't have to believe that this is the specific mutation initially responsible for the inactivation of the gene. I need only note the pattern of shared mutations. Should I want to speculate on the nature of the initial deactivation, this mutation merely presents itself as an obvious candidate.


Tsentralka wrote:
4. There are many single nucleotide polymorphisms (SNPs) shared among haplorrhine GULOs, but not shared with the guinea pig GULO. And the shared haplorrhine SNPs fall in a hierarchical grouping, where each set falls within another set (a nested hierarchy).

Why do you quote this part but not respond to it? It's the crucial point of the matter. The sets within sets, a nested hierarchy of multiple mutations. It follow through prediction logically from an evolutionary progression, but mere design can only ad-hoc it. You wouldn't expect it. And from a statistical perspective, it's incomprehensibly unlikely that multiple lineages all independenly suffered mutations in their GULOP gene and produced an evolutionary nested hierarchy.

Tsentralka wrote:Part 1 here is true…I have no issues. Part 2 (“And the shared…”) requires a good deal of looking into and will be dealt with in a bit.

By all means, go and check the sequence data from the sources, produce alignments, construct the trees and see it for yourself.

Tsentralka wrote:
The real argument lies in the interpretation of the data, yet before we even get to the interpretation, numerous problems have been found with the so-called data itself (namely Fact #3 above).


Furthermore, it is evident based on posts in this thread that some of you have accepted these inaccuracies as the foundation for your belief in why the GULO pseudogene is evidence for common descent. I remind you again of the quote:

Drouin et al 2011 wrote:The nature of the initial mutations which inactivated the anthropoid primate and guinea pig GLO genes is not known.

Which as I say is really a digression and not the true heart of the matter. The nested hierarchy is what matters, the fact that the SNP in exon 10, position 79 is universally shared frameshift causing mutation is really just a cherry on top. It's just a likely candidate.

Tsentralka wrote:Here is another excerpt from evolutionmodel.com.

Image

https://www.dropbox.com/s/tm7ssodg5sg2e91/EvolutionModel.com%20Comparison%20Table.jpg


First the Creationist perspective (right column)…

Point 1 is ridiculous…I’ve never heard a Creationist assume this.

I have, I've had creationists claim instead that the gene is functional but that we just don't know how.


Tsentralka wrote:As you all know from previous posts, I believe humans, haplorrhines, guinea pigs, etc., each originally did have the ability to synthesize vitamin C but it was lost independently in each group

Which would be astronomically unlikely to produce the observed nested hierarchy.

Tsentralka wrote:(as we see happening before our eyes in vertebrates today, i.e. bats, pigs).

And they don't form a nested hierarchy, since the individual lineages each suffer independent mutations in different loci.

Tsentralka wrote:Point 2.1…I agree with the deactivating mutations part.

Good.

Tsentralka wrote:Points 2.2-3 are both based on the inaccuracy of Fact #3 laid out at the beginning.

With respect to 2.2 the assumption seems reasonable to me from what I've heard creationsts say. A typical response I've heard is "common design - common designer" in reponse to shared genetic similarities. Generally the claim is that finding similarities between individual species, both in their genes and phenotypes is expected because, just like with human designers, they sometimes re-use old designs in new things. In that respect. 2.2 is a good representation of a common creationist response, because the re-using or sharing of old designs already used would suggest that we find the same kind of "deactivation" of the GULOP in multiple different lineages, but without a nested hierarchy.

2.3 is just an extension of what I said to point 2.2 about "re-using old designs". If that is what ID/creationists postulate to account for GULOP inactivations, then it would follow that the inactivation was re-used across the board, instead of only used in haplorrhines.

The problem here is that there are multiple different creationist/ID positions, some of which are mutually exclusive. I think the site just tries to answer the more common ones.


Tsentralka wrote:Now the Evolutionist perspective (left column)…

Point 1 is reasonable…that’s also what the Creationist position is.

Well not really. It may be what your position is specifically, but it doesn't follow inexorably from creationism, nor is your position very common.

Tsentralka wrote:Point 2.1 is reasonable…that’s also what the Creationist position is.

Only in so far as you already assume 1.

Tsentralka wrote: Points 2.2-3 are both based on the inaccuracy of Fact #3 laid out at the beginning. So a lot is hanging on the inaccuracy of Fact #3. I’ve contacted the EvolutionModel.com administrator to note this error.

But it's really not that inaccurate. We can't unambigously claim that the frameshift mutation was THE initial loss-causing mutation, mostly because of loss of multiple exons, though it's universally shared presence in haplorrhines still makes it a good candidate. What this does is to make point 2 and 3 weaker points than point 1. It doesn't make it directly false.


Tsentralka wrote:And then comes point number 3.
EvolutionModel.com wrote: Since pseudogenes accumulate mutations from generation to generation, and since the haplorrhine GULOP would have to have been in pseudogene form across many speciation events (and in turn, many common ancestors), we should find shared mutations (again, manifesting as shared SNPs), and we should find that they are arranged in such a way that they give an unbroken line of inheritance for every species (a nested hierarchy).


At this point it dawned on me…we are dealing with a two headed monster. The GULO pseudogene was brought up because the infamous deactivating mutation was supposedly shared between haplorrhines…this is the first head.

And as I explain above, it's really not the main issue. The probabilistic nature of the evidence, the nested hierarchy of sets within sets, and the sheer improbability of producing this pattern through multiple independent degenerations, is the strong point, which you still haven't dealt with.

Tsentralka wrote:The second head is a separate issue altogether, it is the issue of genetic homology…human DNA is similar to chimp DNA, slightly less similar to gorilla DNA, slightly less similar to orangutan DNA, etc.

Yes, the nested hierarchy. The sets within sets. The sheer improbability of it from the standpoint of independent origins. It is not expected, it is only compatible by ad-hoc.
The case must thus be evaluated probabilistically, at which point evolution wins to an unfathomable degree.

Do the calculation, compute the odds of a single mutation happening in a single genome. Now add another mutation, now do it for two genomes, the same mutation twice in two different species, now three, four, five. Keep adding mutations, produce the tree of the nested hierarchy, come back with the odds. The numbers here stagger the mind.

Tsentralka wrote:The switch from head number 1 (shared mistake) to head number 2 (shared SNPs) can be seen in this statement from Inferno:

Inferno wrote:You're confusing all students making a mistake on the same answer (what you detailed above) with all students making the same mistake on the same answers (what I will explain just now). [this is the shared mistake...Head #1] Various animals losing the enzyme wouldn't be evidence, but what if the guinea pigs, birds, bats and pigs all had different sequences from the primate sequences?[this is the shared SNPs...Head #2]


That same switch from shared mistake to shared SNPs occurred in Fact #4 on the EvolutionModel.com and again in Point 3 of the comparison table. This is NOT a criticism…merely a clarification; both heads of this issue are valid points, but I think it better to disentangle them. Anyways, the whole point of this post is to present my thoughts about the shared mistake argument (the first head of the beast). I have presented evidence that we do not know that humans and other haplorrhines shared a deactivating mutation and that arguments which claim they do are based on misinformation. We cannot rule out the possibility that a common mutation deactivated the ancestral form, but the point is that we have no evidence to make this claim…the mutation was more than likely lost along with the other 9 GULO exons.

We don't know that this is more likely. I guess that depends on comparing the total size of the 9 lost exons, to the size of the remaining universally shared GULOP sequence and computing the probability that another mutation happened in one of them and then got lost through a 2nd exon-losing mutation. On the face of it it seems less likely to me, that a hypothetical mutation happened which resulted in the initial inactivation, then subsequenty the exon in question got lost completely.

Tsentralka wrote:I am still considering head number two and will share what I come up with in a subsequent post. Along these lines I wanted to ask a few questions. The evidence presented by Inferno and EvolutionModel.com supporting that more closely related species have more SNPs in common is from the Ohta et al paper which describes nucleotide substitutions in exon 10 (first figure in post). Of course, a substitution is always relative to something (an ancestral sequence in the Evolutionist’s case). Why do you suppose they chose to use the rat GULO exon 10 sequence as the reference? How do we know that the rat sequence has not changed relative to the primate sequence?

The rat sequence is intact and highly functional. It's probably because of all the organisms that still have functional GULO genes, rats are our closest relatives and so would be the species that has the GULO sequence which would be expected to be the most like ours. Likely, this can also be shown by alignments of shared remnants of the haplorrhine GULOP sequence with other, more distantly related species GULO genes. Also, it is likely that rats were also among the species that had at least partially sequenced genomes at the time of the Ohta et al paper, so the rat sequence just presented itself as the best candidiate available at the time. Now that we've sequenced more primates and other species in the interim, it's possible an even better reference candidate sequence for a functional GULO gene could be found. At least, that would be one reason to do it like that.

But without assuming common descent, you could still make the argument on biochemical grounds. Rat physiology and internal biochemistry is more like ours and other primates, than other(on evolution, more distantly related) species are. So it follows that rats also have a GULO enzyme that would fit their internal biochemistry better and by extension, would look more like ours.

Tsentralka wrote:Addendom #3 – Rumraket
I basically agree with your post regarding the nature of the evidence in support for common descent. If I find some out of place ERV or inconsistency I don’t expect it to dent your faith in Evolution.

Well thank you but I have to protest the last part of your comment here. I don't have faith in anything, I go with what seems most likely given the evidence before me. If the evidence is sufficiently weak, then I don't believe the thing in question. I can appreciate and entertain possibilites on matters when pressed to think about them, but that doesn't mean I go out of my way to demand of others that they believe specific things, nor that I go place large bets on them myself or hinge my entire worldview on them.

Allow me a little clarification on this point. Take as an example the origin of life from a modern scientific standpoint. At this stage, we don't know how life originated on Earth(or even if it DID originate on Earth itself, but that's a digression I won't go down atm). The evidence before us from geology and palentology also tells us that there really isn't much evidence left of the earliest stages of our planet. We have very few, minor and scattered clues wich are very general in their nature. Very few, rather inaccurate specifics about the early composition of the atmosphere and crust. With this in mind, we should not expect to be able to say how life on earth DID originate, because we could never find evidence for it in the rocks(supposing the earliest parts of the crust have now long since been recycled through subduction of tectonic platec. etc. etc).

However, scientists do of course speculate on such matters, and they construct hypotheses that attempt to explain how life could have originated, and then test them through various means. To me, that means you should never believe any specific hypothesis, barely on the fact that it concievably explains the origin of life. And in any case, you should only believe that the hypothesis can explain the origin of life, once the hypothesis has sufficient evidential support. I won't go into much detail about what exactly constitutes "sufficient evidence" at this stage, I just want to make sure you understand what I mean when I say I don't have faith, and that I really have to say I disagree with your portrayal when you hint that some deviations can't "den't my faith". I don't do faith.

The reason these minor deviations won't change my stance on evolution is because of the probabilistic nature of the evidence, and the stochastic nature of the process. It's a matter of degree as I wrote to you to begin with. If the case from deviations were to become sufficiently great, and completely overshadow the main pattern of a nested hierarchy, then I absolutely would change my stance on evolution. The only reason this hasn't happened yet is that the case from deviations simply isn't big enough and, at this stage, it's size is actually within the expected range given the stochastic nature of the evolutionary process.

A common creationist mistake is to assume, or overemphasize, that evolution must produce a perfect nested hierarchy with no deviations. That's simply false and there's nothing else to be said on that subject. The case absolutely must be evaluated probabilistically.

With that said, so far I appreciate your response and our interaction. You seem at to me at least so far, to approach the subject with somewhat of an open mind, not out to score cheap points or propagandize, but as a thinking person who considers the arguments and the evidence. You've read part of the first link I gave, which is more than I can say for most creationists I've interacted with, so I thank you for that and of course, I hope whatever you do, at least you can come to see that the case for evolution is very strong indeed. I won't tell you what to believe, go make up your own mind.

Tsentralka wrote:It is a matter of the volume of evidence. However, if I believed everything I heard from Evolutionists, I would be an Evolutionist. I’ve been around the block a few times and I have come to realize that people are prone to misrepresent evidence to support something they feel strongly about (both Evolutionists and Creationists). Your link to EvolutionModel.com is a perfect example. If I had taken their word for everything they said regarding GULO, then I might believe in common descent. Upon looking into it you find several important errors. You apparently did take their word for it and have gone on to propagate those errors (an honest mistake). So forgive me if I am skeptical when you say, “What is actually the case is that there are hundres, sometimes thousands of pseudogenes and ERV's that fall within the expected nested hierarchy, and actually only very few exceptions to the pattern.” We obviously don’t have time to look at all of these, so I am happy to just look at the best representative cases.

Well as I explained above, the error you allude to here isn't so much an error as it's just a likely candidate for the initial deactivation.

I will be looking forward to your response to the more meaty matter, which is the nested hierarchy at large(of which GULOP is really just one such pseudogene example). That really is the main point from the standpoint of comparative phylogenetics.
"Nullius in verba" - Take nobody's word for it. https://en.wikipedia.org/wiki/Nullius_in_verba
Extraordinary claims require extraordinary evidence.
Fri Mar 08, 2013 10:58 pm
TsentralkaUser avatarPosts: 9Joined: Wed Feb 06, 2013 11:41 pm

Post Re: Creationist Inquiry

This is the customary post between posts...nothing "meaty" here, just quick follow-up stuff.

First,

Rumraket wrote:
Tsentralka wrote:Agreed…no issues here…(except that the claim that plants use the same gene/enzyme sounds a little fantastic…I doubt that’s true)


Well, it is. The gene has been found and sequenced in plants too and the protein enzyme purified from them. Here's some evidence:
http://www.ncbi.nlm.nih.gov/pubmed/10050319


Correction noted...thanks for providing that reference.


Secondly,

Rumraket wrote:Why do you quote this part but not respond to it? It's the crucial point of the matter. The sets within sets, a nested hierarchy of multiple mutations.

Rumraket wrote:You're focusing on the wrong piece of the claim....The crucial matter is that it's shared(and it isn't the only one)...

Rumraket wrote:And as I explain above, it's really not the main issue. The probabilistic nature of the evidence, the nested hierarchy of sets within sets, and the sheer improbability of producing this pattern through multiple independent degenerations, is the strong point, which you still haven't dealt with.

Inferno wrote: [You, Tsentralka,] apparently did not deign my posts worthy of scrutiny, even though I showed your point to be wrong before you even made it.


You can only imagine the frustration upon reading statements like these. In fact, I had to go back and check my post to make sure I had actually included the double-headed beast paragraph and not just imagined that I had. See the following quotes:

Tsentralka wrote:Anyways, the whole point of this post is to present my thoughts about the shared mistake argument (the first head of the beast)...I am still considering head number two [shared SNPs/mutations] and will share what I come up with in a subsequent post.



Thirdly (and finally),

Inferno wrote:Drouin et al. do state what you said (“The nature of the initial mutations which inactivated the anthropoid primate and guinea pig GLO genes is not known.”), but it has nothing to do with what you say.


Inferno wrote:Apart from your misunderstanding of what Drouin said...


Inferno wrote:What you showed us is that you misread something that has nothing to do with the issue at hand, ignored evidence contrary to your position from the very same post and apparently did not deign my posts worthy of scrutiny...


Inferno wrote:This, I'm sorry to say, is a highly dishonest paragraph. Aside from the fact that the errors you noted weren't errors to begin with but misunderstandings on your part...


I won't try to defend myself here. I trust the readership to make their own judgement call as to who is misunderstanding the material at hand...Inferno or myself. Although, I am curious...Ramruket, do you think that my use of the Drouin et al quote was dishonest or misunderstood? Please note, I am not asking whether you agree with my position, I am simply asking if you think I misused or misunderstood the Drouin et al quote. Do you understand it to mean what Inferno suggests?

Anyways, one final question for Inferno...

True or false..."Haplorrhine GULO inactivation is likely due to a missing base pair in the amino acid coding region of exon 10, which shifts its reading frame. "

If True...can you indicate the reference or reasoning that led you to this; I have not been able to find such a reference.

Thanks,
Tsentralka
Wed Mar 13, 2013 1:13 pm
RumraketUser avatarPosts: 1170Joined: Fri Jun 25, 2010 7:49 am Gender: Male

Post Re: Creationist Inquiry

It is my estimation that Inferno is the one that misunderstands the statement in Drouin et al.

It seems to me that the Drouin et al. paper simply emphasizes that we can't be sure that it was, in fact, the frameshift mutation in exon 10 that was the original mutation that rendered GULO nonfunctional, since it is concievable that a mutation could have happened in the remaining lost exons, before they got lost ofc.

In this way, what the Drouin et al. paper is saying is that the nature of the initial mutation that caused GULO to go GULOP, isn't known for the reasons stated.

But the frameshift causing mutation in exon 10, position 79 is unambigously a deletion. The fact that it is universally shared among haplorrhine GULOP sequences is, as far as I can gather, what cause evolutionarymodel.org to suggest it on the basis of the data from Ohta et al. It certainly does seem like a likely candidate. To really know this, you'd better check with them yourself. I can only try an work backwards through the same data.

To your specific true/false question, you will notice the key word in their statement: "Likely". I would say yes, it is likely the frameshift causing mutation is the initial loss-of-function causing mutation, and given the data the reasoning I would erect in support of the statement is it's universal conservation in haplorrhines. No, we cannot unambigously claim with absolute certainty that it was. But in the end as I also expressed in my previous post to you, I think that question is ultimately a bit of a digression from the meat.

No, I don't think you were being dishonest or misunderstood the statement.

Also with respect to the response early in my previous post where I ask you to address the meaty parts, I actually started typing out my response to your post as I was reading through it. I later noticed you wrote that your response would be forthcoming later, which I also acknowledged. At that point, I couldn't be bothered going back through my post and pick out the parts where I asked you to address it. For my own part the intention was certainly never to produce any frustrations.

I hope we can proceed with a fruitful dialogue without this becoming an obstacle. Thank you.
"Nullius in verba" - Take nobody's word for it. https://en.wikipedia.org/wiki/Nullius_in_verba
Extraordinary claims require extraordinary evidence.
Wed Mar 13, 2013 5:49 pm
TsentralkaUser avatarPosts: 9Joined: Wed Feb 06, 2013 11:41 pm

Post Re: Creationist Inquiry

Thanks for clearing this up...I suspected this could be the case (replying as you read). and I don't think it is a problem as long as statements such as those I quoted do not stem from a misunderstanding of my post. In your case this is obviously not the case.

Tsentralka
Wed Mar 13, 2013 6:42 pm
LaurensSocial EditorUser avatarPosts: 2950Joined: Sat Mar 20, 2010 11:24 pmLocation: Norwich UK Gender: Male

Post Re: Creationist Inquiry

Addendum #2 – Age of the Earth
Laurens…I’m not going to lie, I did not read your most recent post. Criticize this is you must, but you can’t seriously expect me follow you down your bottomless rabbit trail. I realize that your belief in common descent necessitates your adherence to an old earth, but if your best evidence for common descent is an old earth, then we have some real issues.


Did I make the claim that the best evidence for common descent is an old earth?

I don't remember doing so.

I was saying that macroevolution follows logically from acceptance of microevolution and an old earth. Since you accept microevolution, I showed you evidence of an old earth in order that you might look at it and see that when the two are combined you have plenty of leeway for macroevolution to occur.

Not once did I claim that evidence for an old earth is evidence for common descent, there is much more direct evidence for that. I would appreciate if you did not miss-characterise what I was claiming in future.

Thanks

Laurens
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Tue Mar 19, 2013 4:19 pm
he_who_is_nobodyBloggerUser avatar
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Post Re: Creationist Inquiry

Laurens wrote:I would appreciate if you did not miss-characterise what I was claiming in future.


At least he has actually addressed you and acknowledged your existence. I have posted a few times in this thread and was outright ignored in all my posts.
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Fri Mar 22, 2013 5:55 pm
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Dragan GlasContributorUser avatarPosts: 2954Joined: Mon Dec 14, 2009 1:55 amLocation: Ireland Gender: Male

Post Re: Creationist Inquiry

Greetings,

Welcome to LoR, Tsentralka! :D

A few books are recommended reading as a starting point.

Coyne's Why Evolution Is True for obvious reasons, along with Stringer's The Origins Of Our Species for a understanding of hominid evolution, including our own, particularly in relation to interbreeding (Neanderthals and Denisovans). Ryan's Virolution, though interesting, is not strictly necessary, as information on ERVs is available online.

As regards the "genotype - phenontype" relationship, to retain the - dare I say? - fiction of "kinds", this implies - if not necessitates - a one-to-one relationship, particularly with regard to the special pleading for humans, if not "kinds" in general.

One would not expect to see a many-to-one (convergence) or a one-to-many (ultimately, speciation) relationship - such occurences would lead to questions for the creationist. The fact that hyraxes are most closely related to elephants, phenotypically (morphologically, to be specific) and cows are related to whales - not to mention sea squirts being related to all vertebrates, including humans - is highly problematic for the creationist.

Also, since you're rejecting the non-radiometric evidences for an old Earth, I assume you'll also reject the fact that the observed expansion of our universe, run backwards, results in an age for our universe (if not everything) of ~13.72 billion years?

At some point, you'll likely end up defending the literal interpretation of the Bible and arguments for "God"... ;)

Kindest regards,

James
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"The Word of God is the Creation we behold and it is in this Word, which no human invention can counterfeit or alter, that God speaketh universally to man."
The Age Of Reason
Tue Dec 17, 2013 5:18 pm
jomen112User avatarPosts: 16Joined: Tue Oct 11, 2011 2:33 am Gender: Cake

Post Re: Creationist Inquiry

Tsentralka wrote: I am looking for evidence that all life as we know it evolved from a common ancestor (this is not evolution, though evolution would have occurred during this process).


You may want to take a look at this post.

It takes a little different angle to the whole issue on a broad general level without messing around with all the details but at the same time it brings up a concepts that runs like a red thread though all of life. They key words to remember is nested hierarchies/sets. You will find nested sets everywhere in nature and if you can understand its importance on a broad level it will be easier for you to identify evidence for common ancestor in the detailed and learn to appreciate the enormous amount of evidence that actually exists to backs up common ancestor as a fact.

Imo the fact that nested hierarchies pops up everywhere in nature and the fact that they all, independently of each other, point in the same direction is such a powerful evidence for common ancestor that it simply cannot be ignored.

Once you are convince by the evidence that all life shares a common ancestor then you will appreciate the theory of evolution as the theory that explains how this possible could happen; because we already know, as a fact, that it have happen via common ancestor.
Fri Apr 25, 2014 5:55 am
abelcainsbrotherBannedUser avatarPosts: 774Joined: Wed Jun 04, 2014 6:33 am Gender: Male

Post Re: Creationist Inquiry

Wow! You evolutionists were teaching him so wrong.Have you forgot about the mitochondrial Eve theory and why they came up with it?It is because they did not like what they discovered about primates,neanderthals,apes and man,with apes and neanderthals being more like the primates than man is.So they come up with the mitochondrial eve theory,they refuse to admit life does not evolve and just keep on believing it despite their findings that showed they were wrong.
Mon Mar 16, 2015 6:43 am
VisakiUser avatarPosts: 765Joined: Fri Nov 12, 2010 12:26 pmLocation: Helsinki, Finland Gender: Male

Post Re: Creationist Inquiry

Taking into account how most christians feel about witchcraft they sure do like their necromancy. Well, at least this one does.

P.S. "Apes and neanderthals being more like the primates than man is" is like saying that Lyon is more in France than Marseille.
Mon Mar 16, 2015 9:19 am
jomen112User avatarPosts: 16Joined: Tue Oct 11, 2011 2:33 am Gender: Cake

Post Re: Creationist Inquiry

abelcainsbrother wrote: [evolutionary biologists] refuse to admit life does not evolve and just keep on believing it despite their findings that showed they were wrong.


Yep, keep on living in your fantasy world of denial....
Mon Mar 16, 2015 10:00 am
jomen112User avatarPosts: 16Joined: Tue Oct 11, 2011 2:33 am Gender: Cake

Post Re: Creationist Inquiry

Visaki wrote:P.S. "Apes and neanderthals being more like the primates than man is" is like saying that Lyon is more in France than Marseille.


I doubt ignorant, illiterate Americans (read: creationists) know where France is, even less where Lyon and Marseille is, since it is not mentioned in the Bible. :-D
Mon Mar 16, 2015 10:04 am
VisakiUser avatarPosts: 765Joined: Fri Nov 12, 2010 12:26 pmLocation: Helsinki, Finland Gender: Male

Post Re: Creationist Inquiry

jomen112 wrote:
Visaki wrote:P.S. "Apes and neanderthals being more like the primates than man is" is like saying that Lyon is more in France than Marseille.

I doubt ignorant, illiterate Americans (read: creationists) know where France is, even less where Lyon and Marseille is, since it is not mentioned in the Bible. :-D

.... is like saying Gospel of Mark is more in the Bible than Acts of the Apostles is.
Mon Mar 16, 2015 11:46 am
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