Posted: Oct 31, 2017 10:20 am
by Calilasseia
Been busy with JavaScript programming, so I'm coming to this a little later than I would like ...

Wortfish wrote:
Calilasseia wrote:
Er, no. Darwin was writing in 1859, when there were still large gaps in scientific knowledge compared to the present, and before modern rules of presentation had been formulated for scientific publications. Another 'apples and oranges' comparison, anyone?

Well, the origin of life is still not solved, which is what Darwin was referring to.

The extant research is a good deal closer to the solution than was the case in 1859. That paper you bristled at being a prime example thereof.

Wortfish wrote:
The last of those wasn't a paper, it was a chapter in a book, about the history of molecular biology. Namely, Origins of Molecular Biology: A Tribute to Jaques Monod, a book that moreover was published in 1979. Books tend to have more freedom for poetic licence than scientific papers. Why do I smell apologetic desperation once more?

I missed this one....

Our artificial evolution experiment was performed in a test tube in a few weeks whereas Mother Nature had millions of years to carry out her experiments. This begs the question of whether Mother Nature has explored a similar mechanism to patiently work her evolutionary magic to evolve powerful enzymes from noncatalytic polymeric molecules, like RNA, that were available in the prebiotic world.

Mother Nature patiently performing "magic"? Come on, this paper should have been retracted by the same measure.

Let's take a look at the paper in question, shall we, which is available to read in full via your link? The paper covers, in exquisite detail, how a previously non-catalytic DNA sequence, in the space of a few weeks, was converted into a DNA strand with enzymatic cleavage activity via an in vitro evolution experiment, complete with full documentation of the mutations involved in the transformation. Here's the introduction:

Gysbers et al, 2015 wrote:Introduction

Life would not have evolved and flourished on Earth without the arrival of enzymes, but the mechanism by which enzymes arose from the prebiotic world is an unsolved natural mystery. Life is purported to have surfaced beginning with the self-replication of ribonucleic acids in a hypothetical RNA world1,2,3,4,5. RNA is capable of storing information, and since the discovery of many natural6,7,8,9,10 and artificial11,12,13,14,15 RNA catalysts (ribozymes), the RNA world hypothesis has been found increasingly plausible. Even considering the RNA world hypothesis, the question remains: how did a ribozyme emerge in the RNA world? We postulate that a ribozyme can emerge from a noncatalytic sequence of RNA under permissive evolutionary conditions. To demonstrate this idea, we conducted a test-tube evolution experiment16,17,18 to convert a randomly chosen, noncatalytic sequence of single-stranded DNA, a proxy for RNA, into a catalytic DNA (DNAzyme) with RNase-like activity. Previous ribozymes and DNAzymes have been selected from libraries of completely random sequences11,13,14,15,19,20, or randomized versions of a sequence with a dissimilar function12,18. In contrast, our study aimed to establish a catalyst from a distinct, distant and non-catalytic corner of sequence space. After just weeks, a DNA pool with significant catalytic activity was established. High-throughput sequencing analysis has identified mutations that have enabled the noncatalytic to catalytic sequence conversion. Our findings demonstrate for the first time that an enzyme can arise from a defined sequence of a functional polymer via molecular evolution, a mechanism that may have been exploited by nature to initiate the evolution of enzymes in the RNA world and beyond.

Please take note of that last sentence. Namely, that the authors of the paper demonstrated that a catalytic sequence with enzymatic activity, can arise via molecular evolution from a previously non-catalytic sequence, and did so in the space of a few weeks in their laboratory experiment. Apart from this detonating a nuclear depth charge under numerous creationist assertions, this finding led the authors to ponder whether or not the same mechanism they observed yielding results in the space of a few weeks, would generate the precursor molecules needed to bootstrap life as we know it, given the tens of millions of years of time available for the process on a prebiotic Earth. In the light of this, that somewhat florid sentence at the end of the discussion section, whilst arguable on grounds of taste, is pertinent in the light of the demonstrated experimental results. What part of "could the same molecules that yielded these results in a few weeks in our lab, yield similar results on a prebiotic Earth over a geological epoch" did you fail to extract from the paper? Did you even bother to read the rest of the paper, or did you simply engage in a quote mine fishing expedition?

Wortfish wrote:
Poppycock. The only reason that the staff of PLOS Genetics need to concern themselves with the Declaration of Independence, is where that document exerts legal force over their activities. The funny part being, of course, that early in the history of the Declaration of Independence, the text document was largely ignored, when the matter of constructing the US Constitution was engaging the minds of the relevant historical players. A far more important input into the Federal Constitution, was the prototype Virginia Declaration of Rights. Indeed, historically, the Declaration of Independence was treated more as an aspirational document than a legislative document, and even in the period immediately after the drafting thereof, heavy critique of the disparity between the aspirational statements in that document, and the continued practice of slave ownership by several of the signatories, made its presence felt.

That changed with Abraham Lincoln, who sought to bring legislative force to the aspirational statements, particularly with respect to slavery, and the clash between Lincoln's attempt to turn elevated principle into law, and slave state profiteering from human trafficking, resulted in the American Civil War. Fortunately for those of us who regard slavery as abhorrent, Lincoln prevailed. But, the view that arose from Lincoln's legislative trajectory, and which persists today, is that the Declaration of Independence provides a set of goals that the Constitution should aim to fulfil in law, and that any modification of the Constitution should in turn be directed by those goals. Which is a rarefied part of legal practice extremely far removed from the day to day concerns of journal editors.

Consequently, the need for the staff of PLOS Genetics to concern themselves with this document, from an operational standpoint, is extremely limited.

The Declaration of Independence isn't so much a legal document as it is a political and moral document.

Political, certainly. Moral? Not sure if the original authors intended it to have ethical import, even if some later commentators have chosen to treat it in this manner. But this is irrelevant to the matter at hand.

Wortfish wrote:It declares that all rights come from the Creator , including freedom of speech, which is what a journal is supposed to be faciliating, not obstructing.

Actually, what a scientific journal should be facilitating, is competent reporting of research. Failure to attain certain minimum standards of competence constitute valid reasons for not publishing a paper. Or did you miss this memo?

Wortfish wrote:If the authors thought the data showed the human hand was designed, then they should have been allowed to make this conclusion.

Er, no, you completely misunderstand the whole purpose of scientific papers. Which is [1] to present extant research in the public domain, and [2] to seek validation of that research via the peer review process, though such matters as error checking, etc. I don't pretend that the peer review process is perfect, but it's still massively more reliable than the process we see in the world of apologetics. Having briefly digressed for a moment there, I'll return to [2], which is the matter of import and relevance here. Quite simply, one of the fundamental aspects of peer review, consists of asking the two questions "what assertions are presented in this paper?" and "do the data contained therein support those assertions?". As I've stated on numerous previous occasions, if anyone presented genuine evidence for the "design" assertion so beloved of creationists, the resulting work would be of a standard worthy of a Nobel Prize. If you have to ask why, then I suggest you pay more attention to the elementary concepts I've presented in the past.

Wortfish wrote:
Bollocks. First of all, no one is seriously considering retracting works written in a past era, in accordance with past standards. Second, if those individuals were alive today, they would almost certainly apply modern standards to their output, thus avoiding the issue altogether. Third, what part of "unsupported assertions don't belong in research journals" don't you understand?

What part of "modern standards" allows some scientists to use overtly pagan terms like "Mother Nature" but disallows other scientists from using a general, and not necessarily religious term, "Creator"?

Congratulations on showing your bias here. Last time I checked, the words "Mother Nature" were most frequently used in both everyday discourse, and elsewhere, as a somewhat tired metaphor for the physical universe and its contents. On the other hand, the sort of thoughts that spring to mind much more frequently when I contemplate pagans, is their habit of frolicking in woodlands whilst forgetting their clothing.

On the other hand, the best part of a decade of creationist watching, leads me to be extremely wary when I see "Creator" being introduced into discourse in the requisite contexts. The reason for this, a reason that totally destroys your specious attempt to erect a duplicitous and fake "symmetry" here, being as follows.

Is there a large, well-funded and politically well-connected pagan movement aimed at subverting science? No.

Is there a large, well-funded and politically well-connected fundamentalist Christian movement aimed at subverting science? Yes.

There's your key difference, that destroys your fake "symmetry".

Wortfish wrote:
Did he go on to assert that said appearance was something other than mere appearance? Oh, and by the way, modern research has established that his assertion about apes being unsophisticated in their use of their hands, is somewhat wide of the mark. Modern data provides evidence that non-human apes are not only dexterous, but possess greater intellectual faculties than they were credited with 150 years ago.

Actually, he did so in the same article:

A superior intelligence has guided the development of man in a definite direction, and for a special purpose.

And of course, he was writing in an era before two million peer reviewed papers on evolutionary biology had been published. Which have pretty much rendered supernaturalist assertions surplus to requirements and irrelevant with respect to the biosphere.

Funny how creationist apologetics exhibits such misplaced reverence for the obsolete.

Moving on ...

Wortfish wrote:
Shrunk wrote:
Wortfish wrote:
Keep It Real wrote:"Creator" is anthropomorphic/creationist as it is understood in culture. "Mother Nature" is not as it is understood in culture.

"Nature", on its own, is OK....If someone said Nature did this or that, it wouldn't be a problem. But personifying Nature as a mother goddess is paganism. "Creator" can mean a deity, but it could mean an impersonal principle or force.

Well, OK. If the authors who referred to "Mother Nature" meant the term to refer to a pagan deity, then the papers should have been withdrawn. Similarly, if the paper that used the term "Creator" meant it to merely denote an "impersonal principle of force", then the paper should not have been withdrawn. In all cases, however, the editors came to the opposite conclusions. And those decisions seem quite reasonable to me. Obviously, these editorial deliberations are not required to consider the amount of butt hurt such decisions will cause Wortfish to experience.

They should not have used the word "Mother" to describe "Nature". This reflects a pantheistic belief, not a theistic one.

Once again, as I stated above, last time I checked, the words "Mother Nature" were most frequently used in both everyday discourse, and elsewhere, a somewhat tired metaphor for the physical universe and its contents. Consequently, your assertion does not hold water.

Wortfish wrote:And they shouldn't have referred to any "magic" that she does.

Hmm, why am I and a number of others beginning to smell hypocrisy here?

I'm reminded of the aphorism by Arthur C. Clarke - "any sufficiently advanced technology is indistinguishable from magic". Which could be extended to cover testable natural processes about which we know nothing. That latter extension being, of course, the reason supernaturalism took hold in the first place.

Oh, and I've covered in some depth above, the reasons why your objection here is entirely specious, with reference to the paper's actual contents.

Wortfish wrote:Both authors needed to issue corrigenda.

The only reason I can find for rejecting that one sentence, is for reasons of style. In the light of the published experimental results, it is otherwise pertinent, if rather florid.

Wortfish wrote:Unfortunately, the editors came under enormous pressure to target the "creationists" but not the pagans.

Hmm, let me see ... once again ...

Is there a large, well-funded and politically well-connected pagan movement aimed at subverting science? No.

Is there a large, well-funded and politically well-connected fundamentalist Christian movement aimed at subverting science? Yes.

There's your key difference, that destroys your fake "symmetry".