gcthomas
New member
And apparently I didn't, so who should be reading the rules now?
Real Science Radio 2013: List of Genomes that Just Don't Fit
- Thread starter Jefferson
- Start date
And apparently I didn't, so who should be reading the rules now?
annabenedetti
like marbles on glass
The argument presented is that elephant shrews are closer genetically to elephants than to other shews. That argument makes no other statement on how closely related elephants are to hyraxes or shews. Your rebuttal is ignores the argument.
To wit:
shrew....................................elephant shrew.... elephant
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(I wouldn't expect this, regardless of the veracity of the theory of Evolution.)
Irrelevant.
She claimed that neither of you broke the rules. She was clearly wrong; because one of you clearly did.
Nobody cares if you agree, as you don't make the rules.:dunce::duh:
well once again, Stripey, you are correct. I did not listen to the show. Are you suggesting that Pastor Bob's audio presentation including more information than what was posted? Or suggesting that Pastor Bob really understands what was posted?
I've listened to Pastor Bob before. He either does not understand the underlying science or is dishonest about it. In either case I suspect Jesus is not happy with him.
Alate_One
Well-known member
No, actually it doesn't since the argument is based on a misunderstanding of what the meaning of a common name is, which is basically nothing vs. what the animal in question is ACTUALLY related to. The elephant shrew thing is just as stupid. Just cause it looks like a shrew, doesn't mean it is one.
And the elephant isn't it's closest living relative, it's related to elephants, hyraxes, Sirenians (manatees and dugongs) and aardvarks. Clade Afrotheria for those of you following along.
Playing up only the elephant angle is sensationalism because of the coincidental name.
| Elephant Shrews | |
Alate_One
Well-known member
Well sadly I did listen to some of the show, but it didn't take long for ignorance and classic Enyart cherry picking to rear their ugly heads. Based on what I listened to, there wasn't much need to listen to the show.
For example:
CLAIM: Horses closer to bats than cows . . . citation?
NM I found it: http://www.pnas.org/content/103/26/9929 mind you this is based on retrotransposon insertions only. Things I don’t think YECs accept as indicators of ancestry. Ooops.
And considering retrotransposons are only a portion of the genome, it hardly fits in “genomes that don’t fit” because of course, whole genome sequence has not borne out this relationship. See more recent paper and abstract below – emphasis mine.
Phylogenomic Analyses Elucidate the Evolutionary Relationships of Bats
Current Biology, Volume 23, Issue 22, 2262-2267, 31 October 2013
| Molecular phylogenetics has rapidly established the evolutionary positions of most major mammal groups [1,2], yet analyses have repeatedly failed to agree on that of bats (order Chiroptera) [3,4,5,6]. Moreover, the relationship among the major bat lineages has proven equally contentious, with ongoing disagreements about whether echolocating bats are paraphyletic [7,8,9] or a true group [10] having profound implications for whether echolocation evolved once or possibly multiple times. By generating new bat genome data and applying model-based phylogenomic analyses designed to accommodate heterogeneous evolutionary processes [4,11], we show that—contrary to recent suggestions—bats are not closely related to odd-toed ungulates but instead have a more ancient origin as sister group to a large clade of carnivores, ungulates, and cetaceans. Additionally, we provide the first genome-scale support showing that laryngeal echolocating bats are not a true group and that this paraphyly is robust to their position within mammals. We suggest that earlier disagreements in the literature may reflect model misspecification, long-branch artifacts, poor taxonomic coverage, and differences in the phylogenetic markers used. These findings are a timely reminder of the relevance of experimental design and careful statistical analysis as we move into the phylogenomic era. |
More cherry picking and misrepresentation by Enyart and co. Surprise, Surprise.
Alate_One
Well-known member
And now for the grandaddy claim:
Sponges share 70% of their genes with humans.
Maybe someone forgot that genes make up a paltry 2% of the human genome.
Bob mentions sponges have “genes for nerves that sponges don’t have”. Now why would they have that? Bob says sponges are “genetic libraries” and God keeps reusing stuff and that’s why there are all these crazy similarities (it still doesn’t explain why a sponge *needs* a gene for nerves) He seemed to imply God used sponges as storage for the subroutines not being used yet . . . very odd to say the least.
The "subroutine" idea would almost make sense IF Bob weren’t being dishonest about what “similarities” we’re talking about.
Now if God had done as Enyart suggests and simply used the same “subroutines” in humans and sponges a few thousand years ago we should expect truly IDENTICAL genes in humans and sponges that do the same things. But that isn’t what we see at all. Instead, animals that are proposed by evolution to be closer to humans have genes that are more similar to humans and those that are farther away have genes that are more distinct. There’s a pattern of similarities and differences, NOT a common identical or nearly identical set of toolbox genes/subroutines.
For example, both humans and sponges have collagen to hold their cells together. It’s a basic necessity for a multi-cellular animal. Humans have many different subtypes of collagen. The DNA sequence of those human collagen genes are NOT identical to each other or to the collagen gene of the sponge.
Certainly the sponge has a gene for collagen, and many other genes essential for animal life. Those genes being the 70% of human genes sponges share. But the DNA sequences of the human collagen genes are most similar to those of other primates, somewhat less similar but still similar to other mammals, then even less similar to other vertebrates, more similar to other bilaterians than more primitive animals and so on. So the subroutine idea doesn’t hold up.
Here’s a figure from a paper linked below that shows sponge versions versus other versions of the same class of proteins found in other organisms. You may notice they are not the same and while sponges have some of the same versions, Monosiga (single celled organisms) - has them too.
And you see from the figure below (and I could show thouseands upon thousands of other figures, as well as generate them myself) that show this same simple thing: the more closely related organisms are, the more genes they have in common. In this case we are looking at such divergent organisms, we must compare basic types of genes usually NOT DNA sequence, because the sequences are too different. When organisms are very closely related, we can talk about percent identical DNA sequence.
And here’s a phylogeny based on whole genome data.
Selected organisms from the above phylogeny:
Amphimedon- Sponge (the 70% one)
Homo- Humans
Branchiostoma - lancelet (the one actually closest to humans in the tree)
Drosophila - Fruit fly
Nematostella - Sea Anemone
Lottia - Mollusc
Arabidopsis - Plant
The Paper these figures came from is awesome and a fascinating read. It addresses the roots of multicellularity, implications for cancer and what makes an animal an animal.
I’m pretty sure all of this has been pointed out to Enyart before, but he (and this ignorant guest of his) continue to bamboozle the audience with long lists of things that aren’t accurately reported at all.
Sponges share 70% of their genes with humans.
Maybe someone forgot that genes make up a paltry 2% of the human genome.
Bob mentions sponges have “genes for nerves that sponges don’t have”. Now why would they have that? Bob says sponges are “genetic libraries” and God keeps reusing stuff and that’s why there are all these crazy similarities (it still doesn’t explain why a sponge *needs* a gene for nerves) He seemed to imply God used sponges as storage for the subroutines not being used yet . . . very odd to say the least.
The "subroutine" idea would almost make sense IF Bob weren’t being dishonest about what “similarities” we’re talking about.
Now if God had done as Enyart suggests and simply used the same “subroutines” in humans and sponges a few thousand years ago we should expect truly IDENTICAL genes in humans and sponges that do the same things. But that isn’t what we see at all. Instead, animals that are proposed by evolution to be closer to humans have genes that are more similar to humans and those that are farther away have genes that are more distinct. There’s a pattern of similarities and differences, NOT a common identical or nearly identical set of toolbox genes/subroutines.
For example, both humans and sponges have collagen to hold their cells together. It’s a basic necessity for a multi-cellular animal. Humans have many different subtypes of collagen. The DNA sequence of those human collagen genes are NOT identical to each other or to the collagen gene of the sponge.
Certainly the sponge has a gene for collagen, and many other genes essential for animal life. Those genes being the 70% of human genes sponges share. But the DNA sequences of the human collagen genes are most similar to those of other primates, somewhat less similar but still similar to other mammals, then even less similar to other vertebrates, more similar to other bilaterians than more primitive animals and so on. So the subroutine idea doesn’t hold up.
Here’s a figure from a paper linked below that shows sponge versions versus other versions of the same class of proteins found in other organisms. You may notice they are not the same and while sponges have some of the same versions, Monosiga (single celled organisms) - has them too.
And you see from the figure below (and I could show thouseands upon thousands of other figures, as well as generate them myself) that show this same simple thing: the more closely related organisms are, the more genes they have in common. In this case we are looking at such divergent organisms, we must compare basic types of genes usually NOT DNA sequence, because the sequences are too different. When organisms are very closely related, we can talk about percent identical DNA sequence.
Spoiler
And here’s a phylogeny based on whole genome data.
Spoiler
Selected organisms from the above phylogeny:
Amphimedon- Sponge (the 70% one)
Homo- Humans
Branchiostoma - lancelet (the one actually closest to humans in the tree)
Drosophila - Fruit fly
Nematostella - Sea Anemone
Lottia - Mollusc
Arabidopsis - Plant
The Paper these figures came from is awesome and a fascinating read. It addresses the roots of multicellularity, implications for cancer and what makes an animal an animal.
I’m pretty sure all of this has been pointed out to Enyart before, but he (and this ignorant guest of his) continue to bamboozle the audience with long lists of things that aren’t accurately reported at all.
You seem to have a strange fixation with what Jesus Christ thinks of people. :think:
Based on what we read of yours, there is not much point in reading what you write.
You could follow the link:
| YOU could call it a batty idea, but bats seem to be more closely related to horses than cows are. Once thought to belong to the same group as primates, bats actually belong to the super-order Pegasoferae, which contains horses, cats and dogs, cows, whales and hedgehogs. Within this group, bats were thought to be only distant cousins to horses, but DNA analysis suggests that only cats and dogs are more closely related to horses than bats are (Proceedings of the National Academy of Sciences, DOI: 10.1073/pnas.0603797103). "I think this will be a surprise for many scientists," says Norihiro Okada at the Tokyo Institute of Technology, Japan. "No one expected this." |
This story seems to have subsequently been the reason for more evolutionary analysis:
| By generating new bat genome data and applying model-based phylogenomic analyses designed to accommodate heterogeneous evolutionary processes [4,11], we show that—contrary to recent suggestions—bats are not closely related to odd-toed ungulates but instead have a more ancient origin as sister group to a large clade of carnivores, ungulates, and cetaceans. |
So it seems that if we make a few evolutionary assumptions and accommodate a few evolutionary ideas, we can say something that has no bearing on what was presented in Real Science Radio.
Alate_One
Well-known member
Maybe someone could explain how this makes the presentation "dishonest" or "wrong"?
Sounds like the start of an interesting conversation. You do not seem interested though. :idunno:
There is that word again. You had better have something to back up the charge.
"Truly identical"? Why? Reusing a subroutine does not mean it cannot be tweaked.
Similar design? You don't say. :chuckle:
No similar genes, but there are similarities. :dizzy:
Different types of collagen have different genes. Got it.
Only if we had bought your assertion that a subroutine cannot be changed.
What was inaccurate?
Who knows. :idunno:
I do not want the paper to say anything. :idunno:
I notice you still do not have anything to back up your claim that Pastor Enyart and Fred Williams are "dishonest." :think:
Alate_One
Well-known member
Pretending that having 70% similar genes is the same as having 70% similar or identical DNA. Implication being, chimps are 99% identical, well sponges are 70%!
Alate_One
Well-known member
Try reading . . it helps. :up:
"Genomes that don't fit" while citing mostly papers that are not based on whole genome data, but instead only 2% of it. An intentional playing on the ignorance of his hearers (though this could also be his own ignorance at play) to conflate genes with genome.
The common name basically means that people once thought the elephant shrew was a, uhem, shrew. Including scientists.
How funny it for you to argue "just because it looks like a... doesn't mean it is one." The primary persuasive argument of Evolutionists is that if two species look similar then they are closely related by evolution.
Of course, this "look similar" argument becomes more convoluted as animals were found not to be as physiologically similar as superficial appearances would suggest. And, then more convoluted yet with genetic sequencing.
Scientists once thought the elephant shrew is a shew. Then in the 1800s they decided that the elephant shew isn't a shew, after studying it more closely. And, then in the very late 1900s they discovered the elephant shew was genetically closer to elephants than to shrews. Good luck documenting a prediction of that.
Fred Williams sounds like he misspoke and said "genome" after Pastor Enyart had said "gene" a number of times, however there is no reason to believe that there was any such misrepresentation. Perhaps you could call up and correct Fred on his mistake, but it is wholly unhelpful to assert that the presentation was deliberately misleading.
You can read minds, it seems. There was nothing within the discussion about sponges about chimps. What you need to deal with is what is said, not what you assert has been implied.
How long is the chimp genome?
Perhaps you should call up and point out the problem. :thumb:
:chuckle:
An excellent point. :up:
Alate_One
Well-known member
Nope. Relatedness isn't determined by vague similarity. If it were, people might have considered sea horses more related to horses or perhaps snakes.
Another example:
Closely related? No, not very. How can we tell? But, But, they're similar in appearance! We can examine their skeletons and see major differences hidden in the similar shapes. Ichthyosaurs have vertical tails, and bones that complete part of the fin, while the dolphin's flukes are made only of cartilage. and that's just one example. Examining only the bones can tell us one is a mammal while the other is more closely related to lizards.
In the field of Systematics (classification), relatedness is character based and characters must be selected carefully. And there are entire textbooks devoted to the basics of doing this.
I already told you the connection with fossils. You can't seem to get it into your head.
As a like-kind comparison, if chimps are 98.5% genetically identical to humans, then you'd be a hypocrite to deny they that sponges are 70% genetically identical to humans. But, of course, neither chimps or sponges are actually so close to humans.
If sponges weren't the "most primitive" of animals, you'd swear up and down that "genes for nerves" are vestigial. But, I think we can both agree they serve some function.
As for the Creationist argument, one God, one designer tweaking the same genetic code for various species (with some mutational noise thrown in). Evolutionist arguments are ad hoc. "Humans and sponges share a common ancestor, therefor they have many of the same genes." My problem with that is that given the vast distance between sponges and humans calls for an explanation of why the genes have stayed so similar. Evolution, which builds everything from purely random sources, should leave much more randomness in its wake.
Other than the circular reasoning, what you say isn't really correct. Genetic distances between species do not reflect the proposed evolutionary history of life. The big story isn't that the jumping shrew is genetically more closely related to elephants than to shrews, it's that species tend to be genetically equal distance from other species. For example, the genetic code for cytochrome b protein shows that yeast is 50% related to humans. But, also 50% related to beetles. And, 50% related to turtles. And, 50% related to sea urchins. And, 50% related to pandas. Likewise, all these species are also, by the same measure, equal distant from each other, as the yeast is to them.
Alate_One
Well-known member
This is exactly what I'm talking about. Chimps ARE 90+% identical to humans (across the entire genome) and sponges are NOT 70% identical to humans. They have 70% of the same protein coding genes, which make up 2% of the genome.
Being vestigial would imply that sponges are degenerate from something that HAD nerves. It's possible but it hasn't been supported by the data.
But they aren't actually "genes for nerves" anyway. They're genes for cellular connectivity, which are essential for building nerves. Said genes were repurposed in the nerve building process in animals that have nerves.
The genes AREN'T that similar! But the same TYPES of genes are in both organisms because they're the genes that make organisms multicellular. :bang:
No. Not even close.
The longer the branch lengths, the greater the distance. Humans being closer to monkeys than other mammals but being closer to mammals than other vertebrates. Yeast - Saccharomyces being quite distant from animals. In short. You're wrong.