Profile cover photo
Profile photo
Ration alMind
202 followers -
https://evograd.wordpress.com
https://evograd.wordpress.com

202 followers
About
Communities and Collections
View all
Posts

Post is pinned.Post has attachment
New blog post: a relatively new method by which to quantitatively test universal common ancestry supports the theory overwhelmingly.
I've yet to see anyone really mention this research (aside from a couple of random people in random twitter threads), so this should be new for everyone!
Add a comment...

Post has attachment
Ichythosaurs were warm-blooded and had blubber - they were more convergent to whales than previously known!
Add a comment...

Post has attachment
Turns out it might be fairly easy to define a bacterial "species" after all: www.nature.com/articles/s41467-018-07641-9

The authors performed over 8 billion pairwise comparisons of orthologous sequences between almost 90,000 genomes

The take-home point is that there seems to be a genetic discontinuity in percentage identify when comparing bacterial genome sequences (orthologous genes, really), and that this discontinuity corresponds to the level of "species". This figure from the paper is striking: almost all (~97.5%) of all pairwise comparisons that fell in the range of 76-100% identity were either >95% or <83%. Overall, 99.8% of comparisons returned identities <83% or >95%. There's a severe dearth of pairwise identities in the 83-95% range.

Put simply, if the pairwise comparison between two genomes returned a result of >95%, then the authors show that there's a ~98.5% chance that they're the same species, according to existing taxonomy (barring a few exceptional outliers).
Photo
Add a comment...

Post has attachment
No way I was going to listen to the whole thing, I just skipped to a random time point and listened for a few minutes. Listen between about 1:02:00 to 1:06:00 as +Nephilim Free +NephilimFree lists what he sees as "phylogenetic discrepancies" that disprove evolution. Standing for Truth laps it all up. Here's a quick list of his claims:

Elephant shrews are more genetically similar to elephants than shrews
Horses are genetically closer to bats than cows
Mouse DNA is 80% similar to human genome
Sponges share 70% of human genes
The Kangaroo genome contain chunks of human genome
Neanderthal DNA is fully human
The Chimp Y chromosome is very different to human Y chromosome
Roundworms have 19,000 genes, more than "Darwin could have predicted"
Snake genome contain a quarter of the cow genome
California purple sea urchin genome shares 30% of genes in human genome
80% of human and chimp proteins are different

When rattled off like this, Nephy's list of "discrepancies" might sound impressive to someone with no understanding of biology. However, when you scratch beneath the surface, this list falls apart.

”Elephant shrews are more genetically similar to elephants than shrews”
Yes, Elephant shrews are more genetically similar to elephants (and other Afrotherian mammals) because they are more closely related to them - their shrew-like appearance is only superficial. How is this supposed to be a “phylogenetic discrepancy?”

”Horses are genetically closer to bats than cows”
This was the suggestion of a paper back in 2006 (http://www.pnas.org/content/103/26/9929), but subsequent analyses have failed to support their conclusion (e.g. https://academic.oup.com/gbe/article/9/9/2308/4095375). That being said, the branches involved are quite short so it’s a little difficult to tease apart the relationships. This is a genuine point contention in phylogenetic analyses, although not for the reason that Nephy seems to think. He seems to think this and the previous example are “problems” for evolution because the genetic relationships might not line up with their superficial appearance, which is inconsequential. Superficial appearance isn’t relevant when determining evolutionary relationships - detailed morphological and genetic analyses are.

“Mouse DNA is 80% similar to human genome”
Nephy says things like this a lot, and it’s not clear if he means “whole-genome similarity” or “share 80% of genes”, since he often uses them interchangeably. Either way, he doesn’t explain why this figure is problematic.

”Sponges share 70% of human genes”
This claim is common on apologetics websites and has been made a new low-quality pop-sci websites, and always points back to this paper: https://www.nature.com/articles/nature09201
However, I can’t see anything in the paper that suggests this figure is correct. The closest it gets is reporting that the suite of kinases in the sponge includes about 70% of human kinases, but that isn’t close to the claim that sponges share 70% of human genes period. Again, Nephy doesn’t explain why this finding, if true, would be a “discrepancy”.

“The Kangaroo genome contain chunks of human genome”
This one is an old favourite of Nephy’s. It comes from this interview:
https://www.reuters.com/article/us-australia-kangaroos/kangaroo-genes-close-to-humans-idUSTRE4AH1P020081118
Where one of the senior authors of a kangaroo genome sequencing paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3277949/) said “There is great chunks of the human genome which is sitting right there in the kangaroo genome”. From the context in the interview and also from reading the paper, we discover that she was referring to large-scale synteny being fairly similar between kangaroos and humans, not that there are literally huge sequences of kangaroo DNA that are more similar to human sequences than to other marsupials on the base-pair level. Again, this is not particularly shocking, and doesn’t point to a close human-kangaroo affinity.

”Neanderthal DNA is fully human”
What does this even mean? Define “fully human”. The Neanderthal genome is certainly very similar to modern human genomes, but still clearly distinct enough to be distinguished as different.

”The Chimp Y chromosome is very different to the human Y chromosome”
This is to be expected, since sex chromosomes, particular the heterogametic sex chromosomes like the mammalian Y chromosome, are known to evolve faster than autosomes.

”Roundworms have 19,000 genes, more than "Darwin could have predicted””
Darwin couldn’t really predict anything about genes, since genes weren’t discovered until long after he died, but yes, I suppose it’s true that this is more genes than expected, given that this is roughly the same number of genes as humans have. This was unexpected in the days (several decades ago) when protein-coding genes were expected to be the main determinant of organismal complexity - we know know this is wrong, and that it’s not how many genes you have, but how they’re regulated, that is important.

”The Snake genome contains a quarter of the cow genome”
This is a butchered allusion to another favourite point of Nephy’s: https://www.nationalgeographic.com/science/phenomena/2013/01/01/how-a-quarter-of-the-cow-genome-came-from-snakes/
This is the actual paper: http://www.pnas.org/content/110/3/1012
What Nephy doesn’t understand is that the sequences that make up 25% of the cow genome are all copies of a single element (a single “gene”, if you like). This gene was transferred (probably via ticks) from Squamates (snakes specifically), where it originated, into the common ancestor of all ruminants (cows, sheep, etc). After arriving in the genome of ruminants, it copied itself so much that this single sequence now comprises 25% of the cow genome and similarly high percentages in other ruminants that descended from the original “carrier” of this piece of parasitic DNA. This is really interesting, but not something that calls evolution into question.


The California purple sea urchin genome shares 30% of genes in human genome”
This is a favourite of Nephy’s but again this isn’t somehow a problem for evolution. Nephy again repeats his refrain along the lines of “how can this be, humans and sea urchins clearly aren’t 30% morphologically similar!?” First of all, he’s underestimating the similar between humans and sea urchins. How about the fact that we’re both eukaryotes, so share a suite of eukaryote-specific genes? We’re both animals, bilaterians, deuterostomes - all the characteristics specific to these groups require similar genes! Second, he’s again missing the crucial point that actual scientists have appreciated for decades: just comparing sets of genes doesn’t tell you how morphologically similar 2 organisms should be, understanding their regulation is key. This fact is perfectly consistent with our using phylogenetic based on gene sequences, however, since evolutionary relationships are recorded differently (mostly by neutral mutations) than most morphological changes (by non-neutral mutations, often to regulatory regions instead of protein-coding genes).

"80% of human and chimp proteins are different"
Finally, he repeats another one of his well-worn canards: that 80% of proteins are different between humans and chimps, and that this is somehow incompatible with them being closely related and 95+% genetic identical. For a start, proteins-coding sequences represent about 2% of our genome, so even if 100% of proteins were 100% different between humans and chimps, this wouldn’t contradict the fact that we’re 95+% genetically identical when considering the whole genomes. Nevertheless, Nephy is sure that we should expect 80% of proteins to be identical between humans and chimps for some reason.
His numbers come from this paper: https://pdfs.semanticscholar.org/81ae/4c7e746d5f0c5c0355180ab1bdfea7ce1700.pdf
They compared just 127 human and chimp proteins, finding that 20% (25/127) of them were 100% identical in their amino-acid sequence, and that the other 80% of them differed in some way. They don’t explicitly say how similar the remaining 102 proteins are, but given how they report their results, focusing on those that are 98-99% similar, we can bet that only a very small handful of amino acids differ. In fact, when the chimp genome sequence was published later the same year (2005), they compared about 13,500 human/chimp protein sequences and found that about 29% were 100% identical, and the remaining 71% differed by an average of just 2 amino acid residues. Nothing about this is somehow inconsistent with us sharing a common ancestor. Nephy, however, seems to think that it's impossible for even a single amino acid in a protein to change without being extremely destructive to the organism. Once again he's clueless.

All of this is addressing just a couple of minutes of Nephy's arguments. It took over an hour to gather sources, type up, etc. This is exactly what he does in debates too, gish-gallops all over the place. He's been corrected on all of these claims many times over the years, but of course he's either too stubborn or too stupid to update his spiel.

Fuck you +Dragnauct Sylvas for making me aware of this hangout. I blame you for everything.
Add a comment...

Post has attachment
Johann Hari was a brilliant guest with a lot of interesting things to say on the topic of drug addiction and depression. Also touching on the Trump phenomena. I'll have to check out his books and other works.
Add a comment...

Post has attachment
If you needed yet another reason not to take Answers in Genesis seriously, take a look at this article.

It's about some Pew poll results, focusing on the public's responses to questions about genetic engineering. The first 80% of the article is fine, basically just describing the results of the poll. It wouldn't be out of place on a generic popular science website.

But then in the last section, the obligatory AiG spin has to be added. And what a spin it is. The author says that since the questions were about animal research, this implicitly assumes that we humans are separate from animals, and that we have power over them (the ability to genetic engineer), just like the bible says!

We find quotes like:
"In an evolutionary paradigm where humans are merely animals, why would you bother polling animals about other animals?"
and:
"If we are all just animals, and we carry that thought through every facet of life then this poll makes no sense. The very fact that the pollsters did this survey at all shows that they (and we) know deep down inside that there is a creator God and that we are separate from the animals (Romans 1:19–25)."

Add a comment...

Post has attachment
An important new study on ancient proteinaceous soft tissue preservation has just been published.
+Nesslig 20 +Jackson Wheat
Add a comment...

Post has attachment
I opened iMovie for the first time in 6 months and found this cued up, thought I may as well share it.
Add a comment...

Post has attachment
At 46:30 in this video, of Michael Behe giving a presentation about ID, he says "If it looks like a duck, and if it walks like a duck, and it quacks like a duck, then I am justified in thinking that that is in fact a duck."

Sound familiar? I wouldn't be surprised if Ronnie picked up that little rhetorical device from Behe there. There's a comment from Tommy Hall under the video, so I think it's pretty plausible that Ronnie watched it too.

Just an observation.
https://www.youtube.com/watch?v=hIy7BhVgPCs
Add a comment...

Post has attachment
Wait while more posts are being loaded