Wortfish wrote:aban57 wrote:Wortfish wrote:So, it is OK to say Evolution did it, Mother Nature did it....but to claim the Creator did it is a no no. This is despite the fact that a "Creator" is mentioned in the Declaration of Independence for the United States.
What does this have to do with anything ? You can find millions of references to Santa Claus, doesn't make it real. A paper trying to explain a natural process invoking a fictional character can't be taken seriously, no matter which character is used.
Darwin himself referred to the "Creator" in the Origin of Species:
There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.
So, by that token, Darwin would have his scientific contributions withdrawn. This is madness.
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?
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.
As for the crystallography paper, well, lo and behold, what do we find when we look at the paper in full? Oh wait, we find this:
Pemberton et al, 2012 wrote:A motivation for the current study is nature’s use of the amino acid l-proline as a cryoprotectant. Plants accumulate proline in response to environmental stresses, including freezing temperatures (Hare et al., 1999; Yoshiba et al., 1997; Szabados & Savouré, 2010). For example, early studies on coastal bermudagrass shoots showed that drought stress caused an increase of proline from less than 0.1 mg per gram of dry weight to over 15 mg per gram (Barnett & Naylor, 1966). Also, a 500-fold increase in free proline to levels as high as 60 mM has been observed in water-stressed tomato-plant cells (Handa et al., 1983). Proline also protects yeast against freeze stress (Takagi, 2008; Morita et al., 2002; Takagi et al., 2000). Gene-knockout studies have shown that disruption of proline catabolism in yeast improves freeze tolerance and that the mutant yeast strains accumulate up to 9% of the cell’s dry weight in proline (Takagi et al., 2000). In addition, the freeze tolerance of certain fly larva is a consequence of elevated levels of proline (Kosˇta´l et al., 2011, 2012). In some cold-acclimated larvae, for example, the proline concentration reaches 147 mM (Koštál et al., 2011).
Namely, deeper in the paper, we find that l-proline
has been observed repeatedly acting as a cryoprotectant in a range of natural systems, ranging from tomato plants through fly larvae to yeast cells. All observations provided with relevant citations.
The authors then go on to cite prior art, in which l-proline was pressed into service as an
in vitro cryoprotectant in the laboratory, viz:
Pemberton et al, 2012 wrote:The role of proline in freeze tolerance
in vivo has prompted the use of the amino acid in the cryopreservation of biological samples
in vitro. For example, cultured cells of maize have been freeze-preserved in 10%(w/v) proline (Withers & King, 1979). Also, proline at 27 mM has been used for the preservation of ram sperm (Sánchez-Partida et al., 1998). Additionally, low levels of proline [1%(w/v)] have been used in conjunction with other solutes in the cryopreservation of human stem cells (Freimark et al., 2011). To our knowledge, proline has not been used as a cryoprotectant for protein crystals.
That last sentence, of course, is the lead-in to the authors' own research, namely using l-proline as a cryoprotectant for protein crystals, which, prior to their work, was not a documented laboratory use of this material. Which they then introduce in the next paragraph thus:
Pemberton et al, 2012 wrote:Here, we demonstrate the use of proline in the cryoprotection of crystals of hen egg-white lysozyme, xylose isomerase, histidine acid phosphatase and 1-pyrroline- 5-carboxylate dehydrogenase. Proline was found to perform as well as traditional cryoprotectants in these cases.
In short, the statement that l-proline is a naturally occurring cryoprotectant, suitable for use in the authors' own research, isn't presented as a blind assertion, but
as a documented fact, accompanied by citations of said prior documentation of that fact. Whilst the use of non-rigorous language in the title and abstract is an issue to be addressed, it isn't introduced in the form of a blind assertion, and no one other than certain florid pagans uses 'mother nature' except as a shorthand for 'the observable universe and its contained phenomena'.
But these elementary concepts were doubtless deliberately ignored in the generation of the requisite apologetics.
As for the first paper in the list, that wasn't a research paper, it was a news article, and clearly labelled as such on the web page, or did you miss the words "news and views" immediately above the title of the article?
Here is the article in full. Let's see what it says, shall we?
Crystal, 2002 wrote:When gene therapy was evolving as a therapeutic concept in the mid- to late1980s, the initial vision was to correct hereditary disorders by replacing the abnormal gene, or at least its mutated segment, with the normal sequence. But despite major technological gains over the past 15 years, homologous recombination at the DNA level has not been achieved at a sufficiently high frequency for treating human genetic disorders. An alternative approach being pursued by several groups is to attack the problem at the RNA level. One strategy, known as "
trans-splicing", involves transferring a DNA sequence coding for an RNA decoy that fools the cell into combining the decoy RNA sequence into the relevant messenger RNA (mRNA) as the cell processes the pre-mRNA into the mature message. (Fig. 1). In this issue, Li
et al1 use
trans-splicing to correct
in vitro and
in vivo models of the cAMP-sdependent Cl
- channel abnormality of the airway epithelium that characterises cystic fibrosis.
Cystic fibrosis is an autosomal recessive hereditary disorder characterised by lung and pancreatic disease and by infertility in males
2. The disease manifests itself when mutations in two parental cystic fibrosis transmembrane conductance regulator (CFTR) genes are sufficient to reduce CFTR levels and or/function in exocrine epithelia to <10% of normal
3. Liu
et al1 hypothesised that the consequences of the common ΔF508 mutation in exon 9 of the
CFTR gene could be corrected in airway epithelia by transferring to cells a mini-gene coding for a decoy RNA molecules that mimics the 3' part of intron 9, followed by the normal coding sequences for exons 9 through the remaining 3'-CFTR coding sequence. Using a recombinant adenovirus vector to transfer the DNA sequence of this decoy to human cystic fibrosis ΔF508 homozygote polarised bronchial epithelia
in vitro, they restored the cAMP short-circuit current (a parameter that measures the CL
- conductance of the CFTR molecule) to 16% of that exhibited by normal bronchial epithelia. Molecular analyses confirmed that the decoy functioned as predicted. This strategy also partially restored CFTR function in human cystic fibrosis bronchial xenografts in nude mice, an
in vivo model that mimics the dysregulation of CFTR using airway epithelial cells derived from the airways of individuals with cystic fibrosis.
The rest of the paper then goes on to explain the rationale for Liu
et al's work, which is the primary citation in the news article.
My remarks about language use in the previous paper apply here also, but with less force, because it is not a research article itself, but a news article.
Why do I smell apologetic desperation once more?
Moving on ...
Wortfish wrote:Calilasseia wrote:Who fucking cares about this? The Declaration of Independence isn't a scientific document, and was furthermore written in an era when supernaturalism still exerted undue control over discourse - an era before science had rendered mythological assertions irrelevant with respect to vast classes of entities and phenomena. If citing this document is the best you can do, it's a measure of your apologetic desperation.
PLOS genetics should care since it is a journal published in the United States and the DOI is a foundational document of the US for all its citizens.
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.
Wortfish wrote:And, as I pointed out, Darwin himself referred to the "Creator" who breathed life into the first organism.
Dealt with this duplicitous apologetic elision above.
Wortfish wrote:Thomas Jefferson and Charles Darwin would be forced to retract their works by a scientific community that refuses to even countenance the very possibility that the human hand was designed intentionally.
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?
Wortfish wrote:Oh, and Alfred Russel Wallace made the same claim in his own tract on the subject:
http://people.wku.edu/charles.smith/wallace/S165.htmThe hand of man contains latent capacities and powers which are unused by savages, and must have been even less used by palæolithic man and his still ruder predecessors. It has all the appearance of an organ prepared for the use of civilized man, and one which was required to render civilization possible.
Ahem, let me highlight the important part for you, viz:
all the appearance of an organ prepared for the use of civilized man
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.
But I don't suppose any of this will bring a halt to your apologetics, will it?
by 
