Saturday, May 2, 2015

Sorry You Are Blocked From Quanta dot Org Magazine



[**Update: 5.3.2015 The Chief Editor of Quanta responded to my letter, (within 24 hours), which you can see at the end of the article. Quite honestly I have not experienced that sort of thing before, on a public web site (and I've been attacked by nasty troll commentators) but a "block" especially on a site you like, is far worse, and I was certainly "shocked" and dismayed if not blown away by the notice. Thankfully, it was a "glitch" as explained by Quanta, and so was all "much ado about nothing" and we can move on to the more exciting and relevant scientific issues!]




Telling someone to go "F%$k Themselves" on a blog is generally very bad behavior. But if you block someone from a public web site, particularly when they are a scientist who has carefully complied with your 'rules', and is obviously well intentioned, well, that is dropping the NUKE and that's a lot bigger than FU. Well, that's exactly how it felt to get this notice. Think about it "You are unable to access Quanta Magazine.org". I like Quanta Magazine, so you can imagine my reflux when I found this pop up the next time I logged in:






I have no idea what I could have done to warrant such a notice and I was frankly quite stunned to see it from Quanta. Furthermore, I noted that my comments which were pending on the Quanta site, were removed without being posted. I was attempting to participate in what I believed was an open, public discussion about science in a professional manner. I have inquired as to what is the justification. Fortunately I saved these (below). It is, in my opinion, simply unacceptable to say the least. My opinion of Quanta Magazine has taken a nose dive. I will post this experience and see what readers think.

Here is the first paragraph of the Quanta Magazine articlehttps://www.quantamagazine.org/20150416-how-structure-evolved-in-the-primordial-soup/:

“About 4 billion years ago, molecules began to make copies of themselves, an event that marked the beginning of life on Earth. A few hundred million years later, primitive organisms began to split into the different branches that make up the tree of life. In between those two seminal events, some of the greatest innovations in existence emerged: the cell, the genetic code and an energy system to fuel it all. All three of these are essential to life as we know it, yet scientists know disappointingly little about how any of these remarkable biological innovations came about.”

“It’s very hard to infer even the relative ordering of evolutionary events before the last common ancestor,” said Greg Fournier, a geobiologist at the Massachusetts Institute of Technology. Cells may have appeared before energy metabolism, or perhaps it was the other way around. Without fossils or DNA preserved from organisms living during this period, scientists have had little data to work from.

That basically sums up the remaining article or at least the points that I took issue with. I underlined the most speculative aspects, the ones that need lots of references. One notes key phrase like “It’s hard to infer…” events before the last ancestor. What does Ancestor mean? He’s referring to a molecule, not Neaderthal Homo Sapiens. Not to mention that the first paragraph is highly speculative to say the least if not bespeaking a critical lack of knowledge about the ONGOING pressing debate of this field (misleading the reader to believe the story is well known or accepted by scientists). I was not the only commentator to point these issue out.

Here is my response:


Regarding the paleogeology, these are no doubt feats of biochemistry performed by Greg Fourneir’s group, however to the very first point “molecules replicate themselves” I believe there is a much larger problem here, which seems to be entirely overlooked, and that is energy or entropy, which are intricately linked. We don’t have evidence to support the notion that chemical systems can decrease their entropy, nor can they pump out entropy. The consequence is that they undergo a “heat death.” Since this article deals with primordial groups of molecules, I’m not sure that “mutation” is really a term that applies chemically, and it’s not clear what sort of mutation “beneficial, harmful, or neutral” would allow these molecules to overcome diffusion or heat death. I explore such issues in http://causaldistinctions.blogspot.com/2015/04/a-speciric-reply-to-paper-in-which-i.html?showComment=1429833663020#c921466593852687181

 

When another commentator attempted to respond to me, (see his response below) what is very clear is that his understanding of chemistry or physics is rather limited, and I also was obligated to reply to his factual/scientific error in comparing among other things, dissimilar physics of refrigerators to chemicals.


However, when I attempted to respond to “Jon”, I got the rather nasty notice I copied here. “Sorry, you are blocked from accessing Quanta…”

 

Does this justify them blocking me from the Quanta Org ? No obviously not, no justification was provided. I still have no idea what prompted this very surprising reaction from Quanta and somewhat hostile treatment directed towards me personally (and not the other commentators). But what I later realized is that the author/editor of the article, Emily had also commented in the post, so now things are beginning to make more sense.

As you can see it is fairly obvious that Emily knows the scientist personally, she asked the scientist to comment on another commentator. Emily Singer says:

 “@charles, thanks for your comment. Genetic mutations are generally random and can have a positive, negative or neutral effect.” –Emily Singer

And again, that was one of my points, Singer is simply so far off the mark it’s not even science we’re talking about, molecules do not have different mutations, nor was Charles talking about the article, (which is protein chemistry) it’s not clear WHAT he was talking about, but Charles comment is not blocked. Singer only demonstrates that she is partial to some and not so much to others.

So there obviously is no justification, and it smacks not only of active blocking of potentially contrary but scientific viewpoints, but also of frankly “conflict of interest”.

I wrote a (friendly) response to the author/editor of the “thread” see below, explaining the situation.

Dear Emily Singer,

I noticed that my replies to the other commentator "Jon" were unfortunately removed from the Quanta comment feed. Can you please explain why these were removed, or return my comment to my email provided? I was attempting to reply to the scientific points, and to clarify scientific or factual error. Jon did in fact conflate the notions of how molecules would operate vs a mechanical device, and obviously doesn't understand the physics. A "mutation" has no chemical definition that I'm aware of, nor does "better functioning" molecules. I would hope that this is a mistake and that Quanta does not edit out valid scientific or correct and factual commentary from its magazine. Thank you, Matthew Kosak

The editor DID in fact, re-post my original comment so that I could see it (and you can too) before it was deleted. It really DOES appear to be vile doesn’t it?

Jon, good points, however that is quite a leap made between molecules to refrigerators. I was actually referring to a pre-biotic system, a natural aggregation of molecules (or presumed aggregation?) likely in the ocean or other body of water. It would not have a boundary of any kind. Certainly based on what is known (bench-wise) about chemical processes, collections of molecules don’t remove heat or excess entropy, like refrigerators do. I discuss some issues relating to this problem here: (I list my link..)

Conclusion: I’m not sure this is JUST a situation of Quanta censoring out other relevant scientific commentaries for no valid reason OR, if it is simply the lead author Emily Singer going on some kind of vindictive, self-interested war path against well meaning commentators attempting to participate in the real scientific debate. Maybe she is just covering up her factual errors? That hardly seems justified. She was clearly beyond wrong about “mutations” having anything to do with molecules (see comment section), or having one iota of evidence in the article to support it, so I suppose the best thing would be to censor and block that. Why not?! Right? But one thing is clear, getting that SORRY YOURE F%$*ED-BLOCKED notice is just plain nasty and below-the belt and Quanta Magazine should absolutely explain what happened.
[**Update 5.3.15 Quanta responded to my letter:


Hi Matthew,

There appears to be a technical glitch that is preventing some readers from accessing QuantaMagazine.org. We received at least one other complaint from a reader who said they were “blocked” from our site. Please be assured that we have not purposefully blocked anyone from viewing our site and that we’re working with our developers to fix the issue.

Regarding the comment that you referenced in your note to Emily Singer, it was awaiting moderation (which is why it had yet to appear on the site). The comment has now been moderated and approved.

Best,
Thomas Lin

-- 

Thomas Lin
Editor in Chief, Quanta Magazine

SIMONS FOUNDATION
I have to say that Quanta Magazine has "restored themselves" in my view, as a leading web-science publication, and I thank Thomas Lin for his letter and taking the time to look into the glitch. I also have to eat some of the words, (I'll recover), but I hope that it serves as some guidance for others who might experience similar issues in the future. Now, (sigh) we can get on with the exciting scientific issues!! that are turning upon this dialogue over on Quanta.
 
1.  Regarding "self-replicating" molecules here's a good article-

And their conclusion regarding RNA replication (2013) was the following: "It's great progress, but the result still comes far short of a molecule that can copy itself. For one thing, the ribozyme tended to stop short of the end of the molecule it was copying, mostly because the two fell out of contact."

 
 
 

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