Sunday, February 28, 2016

125 Rebuttals, #5

Alright, just a reminder, I'm rebutting the logical fallacies contained within the arguments found here.

5: The Argument of the Ancient Protein as the Origin of Life

Well, if past performance is any indication, this is going to be an interesting one.  Wonder how PSH is going to define 'ancient protein.'  
1. The primeval proteins, described (Aug. 8. 2013) in the journal Structure, could reveal new insights about the origin of life, said study co-author José Manuel Sanchez Ruíz, a physical chemist at the University of Granada in Spain.
Alright, so first, we need a source.  Unfortunately, PSH doesn't know how to do anything other than copy and paste text from other people, so I had to go and find it on my own.   The article doesn't contain the word primeval, though it does contain the phrase 'origin of life' three times.  For some context, here's one of those quotes:
To summarize, we have shown that protein 3D structure determination can be reliably carried out with laboratory resurrections corresponding to Precambrian nodes dating up to approximately four billion years ago, i.e., close to thThis leads me to believe that, since the author of the blog post didn't simply just link to the blog, that it is indeed a plagiarism.  Seeing as how the arguments mostly appear to exist on that blog, I'm going to switch gears here.e origin of life. This result is remarkable, given the large number of sequence differences (up to ∼50%) between the extinct and extant proteins, and demonstrates the possibility of incorporating a time scale of several billion years to expand the sequence space for 3D structure determination studies, i.e., a time scale over which we may expect significant changes in protein structure to occur. We have furthermore shown that critical evolutionary issues regarding fold definition, fold age, and the identification of ancestral and derived structural features can be readily addressed based on putative ancestral structures. The results and analyses reported here thus support that laboratory resurrection targeting Precambrian nodes followed by 3D structure determination can be a powerful approach to explore the poorly understood evolution of protein structures.
Journal, Conservation of Protein Structure over 14 Billion years, Aug 8 2013, Paragraph 9
So, the statement made by PSH, ripped once again from the Proofs of God's existence blog, doesn't carry any such citation either, just a literal rip of the argument.  The ultimate post does indeed include a link, so I guess that counts as attribution.  Since I can't say whether it's the blog owner's post or not (though it seems to be at this point), I'm going to work from the premise that it is, and continue in this vein.

As you can see by the quote from the article, and the article itself, 'primeval proteins' aren't mentioned.  It's actually not even talking about RNA as the origin of life, since it's actually talking about the fact that they were close (i.e. after) to the origins, not the actual origins themselves.  This is so intellectually dishonest, and such a false premise, that I shan't dwell on it any longer.
2. Exactly how life emerged on Earth more than 3 billion years ago is a mystery.
Wonderful. Good thing you pointed out that, in fact, you do not know.  Again, argument from ignorance fallacy, possible poisoning the well / guilt by association.
Some scientists believe that lightning struck the primordial soup in ammonia-rich oceans, producing the complex molecules that formed the precursors to life.
It's possible that electricity helped catalyze some reactions, but it ignores the fact that things like table salt form without it, and are natural, self-replicating procedures.  Lightning didn't just strike a salt bath and make bacteria.
Others believe
that chemical reactions at deep-sea hydrothermal vents gave rise to cell membranes and simple cellular pumps.
Again, who?  Also, it's possible, so it's got that going for it, which is nice.  I mean, the hydrological activity wasn't what created it, but rather chemical reactions that were permitted by the conditions, but I digress.  It's probably just bad wording.
 And still others believe
Seriously, PSH, it doesn't matter what people believe. It matters only what can be shown with evidence.  Some people believe that gnomes steal their underwear, but like any belief, it doesn't mean anything here.  Unless you're meaning the other definition of belief, which requires evidence.  Which you don't, which is a modified fallacy of ambiguity.
that space rocks brought the raw ingredients for life — or perhaps even life itself — to Earth.
And again, that's something that may have happened, but as I discussed yesterday, whether it was panspermia or not, that's not even part of the question at this point, because those organisms had come from somewhere. Imagine I purchase a cake.  The cake is in my house.  It was somewhere else.  Taking this analogy one step further, it's a bit like saying that since cakes come from stores, the wheat used for the flour didn't have to be grown.  It's a non-sequitur, plain and simple.  This argument is invalid here, for one because this is supposedly a premise, and  for two because it doesn't address origins.
3. It seems that the complexity of thioredoxin, a class of small redox proteins known to be present in all organisms, suggests intelligent design.
    a. They then recreated the protein in the lab. The original “fossil” protein was incredibly stable, bound to many different chemicals and functioned well in a highly acidic environment.
    b. “That makes a lot of sense because 4 billion years ago, many people think that the temperature was high and the oceans were acidic,” Sanchez Ruíz told LiveScience.
Well boy howdy, what do you know.  The article PSH is referring to here is literally where the quote from the first premise was ripped from.   Also, literally the first few points.  What a disingenuous bastard PSH is.  This is literally the definition of plagiarism.  Same goes to that Proof of Goddamn But The Author Is An Imbecile blog or whatever.  The LiveScience article is discussing something in a different context.  Again, the argument made by PSH is that ancient proteins might be the origin of life.  The article from LiveScience is dealing with the fact that the proteins were recreated.  Which is what we'd expect if the guys doing the science are on a correct hypothesis.  It's important to note that LiveScience is not a peer-reviewed journal, but rather an interesting place to read up on science.  This is a great example of how a statement can support one thing in one context, but not another thing in another context.  This, folks, is why it's important to give proper attribution and context to whatever sources you rip from.

Think for a second, about what I've just done.  I'm arguing points on a forum thread post, ripped verbatim from a blog without attribution, ripped verbatim from a science news article without attribution, to support a claim where no claim was made in the original context.  This kind of mental gymnastics is Olympics-level stuff, if the Olympics were giving prizes to the worst offenders.

Let's do some rapid-fire stuff on the next few points, since it's basically the same tripe.
4. A BBC article pointed out several problems with this resurrected theory.
Which article, and which theory?  For crying out loud, you'd think if this were important to the point, PSH would at least link to it.  Maybe it's not really terribly important.  Luckily, our fair PSH's morals don't change in a few sentences, so finding the article was relatively simple. To their credit, the BBC really seems to cover this better than LiveScience.  Also, that statement is pretty much a lie.  Here's an actual quote from the article.
    a. Prof Eric Gaucher of Georgia Tech, US, helped with the ancestral gene sequence reconstruction and commented: “A gene can become deactivated by as few as one or two mutations.
    b. “If our ancestral sequences were incorrectly inferred by having a single mistake, that could have led to a dead gene. Instead, our approach created biochemically active proteins that fold up into three dimensional structures that look like modern protein structures, thus validating our approach.”
Here, let me put that in context.  From the selfsame BBC article:
They then used modern bacteria to convert the ancient gene sequences into a chemically active protein that could be measured to determine its molecular structure and the properties of the ancient protein.
The thioredoxin protein is an enzyme which can break sulphur bonds in other molecules and has a number of metabolic functions in cells. It is shared by almost all life on Earth, from the simplest bacteria to complex animals including humans, indicating that the ultimate single-celled ancestor of all life on Earth would also have had the gene.
Prof Eric Gaucher of Georgia Tech, US, helped with the ancestral gene sequence reconstruction and commented: "A gene can become deactivated by as few as one or two mutations.
"If our ancestral sequences were incorrectly inferred by having a single mistake, that could have led to a dead gene. Instead, our approach created biochemically active proteins that fold up into three dimensional structures that look like modern protein structures, thus validating our approach."
The group used molecular clocks to date the evolutionary branches back in time and linked them to geological changes in Earth's environment.
Changes in the protein's length appeared to occur in fits and starts, with its helix structure suddenly lengthening at the point that cells started to develop a nucleus (the transition from prokaryote to eukaryote), paving the way for higher life.
The results suggest that biological systems might evolve at the molecular level in discrete jumps rather than along continuous pathways, as has been suggested from studies of the evolution of species. 
This quote is pulled so vigorously out of context that the actual context of the quote argues against the point PSH is trying to make.  This is called quote mining, cherry picking, or the fallacy of incomplete evidence, among others.
5. Even bigger problem is the dismissal of the main tenet of neo-Darwinism namely the gradual evolution.“The results suggest that biological systems might evolve at the molecular level in discrete jumps rather than along continuous pathways, as has been suggested from studies of the evolution of species.”6. Finally, Sanchez Ruíz has a great doubt whether the designed protein in the laboratory had anything to do with a hypothetical lonely protein in an imagined hot sea:“There is no way to make absolutely certain unless we invent some kind of time machine…But we know that the properties we measure for these proteins are consistent with what we would expect of 4-billion-year-old proteins.”7. One more problem of this earliest thioredoxin protein is that it is not simple, but complex, stable, and possessing multiple functions. And what would it function with, if not a cell filled with many other proteins and genes? 8. Another speculation in the theory of Ruiz is that thioredoxin arose on Mars and then was transported to Earth in meteorites.  “Four billion years ago Mars was a much a safer place than Earth…Maybe we have resurrected Martian proteins. Maybe the last universal common ancestor (the first life) formed on Mars and transferred to Earth.” 
And the rest of that is exactly the same.  Apart from being unable to stick to one piece of evidence, now our brave PSH (and I'm presuming the PSH in the forum is the same as the PSH from the blog, now.  I'm thoroughly convinced now he's disingenuous enough to plagiarize himself and not realize it) takes quotes from those sources and mixes them up, destroying context to paint a picture that doesn't exist.  Literally, what he's doing is akin to this, taking literal segments and making them say something else:
Fair use fair use fair use....
But I'll remove if it they want me to.
I don't like simply ripping off other people.

Am I really going to do all 125 of these?  Sometimes it seems hard, but I honestly enjoy it. One of the hard bits of doing something that was written completely, at some point in the past, is that sometimes it feels like I'm just repeating myself over and over and over...
9. However, no life or products of life have yet been discovered on Mars, and shifting the origin of thioredoxin from earth to Mars still does not explain how a complex protein arose at once.
 That's right.  The cake analogy from above.
10. All in all, after considering all the impossibilities and unexplained things, intelligent design by the greatest designer who all men call God is the best explanation.
Oh, and we did it again.  Again I shall remind you, gentle readers, that not one shred of evidence was given in support of anything.  Even if we take the arguments at face value, and pretend that they are arguments against the premises presented therein, no premise of a false dichotomy was even introduced here.  Not once did PSH provide one shred of evidence that some other method of nature could produce it, nor that it could simply have existed for ever.  Nowhere does he provide a single premise in support of any god, let alone his own.  This is the simple appeal to heaven fallacy, or the god of the gaps fallacy more specifically.

The presumption is, if someone can't explain something to one particular individual, that somehow invalidates the reasoning of the argument.  Here, however, we actually do have a neat dichotomy.  It's entirely possible that it's being explained correctly, and PSH is simply too daft to understand it.  Well, that's not really a dichotomy per se, because there are other options.  Perhaps PSH is simply willfully denying, or is too dishonest to allow any honest ideas into his mind.

Tune in next time when we tear down another fun, logically incoherent argument.  Speaking of which, I almost forgot.
 11. God exists.
Actually, I'm not quite done. There's one more fun logical structure I can throw in here.  Also, I just realized, this argument for god actually runs contrary to Irreducible Complexity, since PSH is letting it be valid that they did, indeed, replicate the RNA structures in a simpler way.  Remember, this is one of the foundational points of this set of premises.

acce245's Argument that Some Other God Exists

  1. Creationists can't seem to agree what god exists.
  2. There's tons of evidence that maybe their god doesn't exist.
  3. Buddhists think Yahweh doesn't exist.
  4. Christians think Allah doesn't exist.
  5. Muslims think Yahweh doesn't exist.
Conclusion: None of those gods exist.  Ergo, leprechauns must exist, because they created the universe.

I'm sure I won't change PSH's mind, but if you want a fun argument to throw around with a creationist, have fun!  Just remind them, those same scientists they quote will likely be deistic, if religious at all, and they also claim that PSH's god doesn't exist.  It's a fun way you can apply learning in your daily life.

Peace to all of you, and until next time, think rationally!

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