rationalskepticism.org

Wortfish wrote:

Calilasseia wrote:
This is such a blatantly duplicitous reply, that it's barely worth dignifying with a response. But in the interests of rigour, I'll provide one. Quite simply, if the data says that the authors have jumped to incorrect conclusions, then that is the criterion for rejection. Which is an essential part of those scholarly standards you're mendaciously seeking to dismiss, with this egregious misrepresentation of peer review as being in any way "symmetric" with apologetic fabrication.

In case you hadn't worked this out, this is the whole point of presenting scientific papers - so that others familiar with the proper treatment of data can spot and report errors to be corrected. Indeed, examples of reasons for rejection of papers have been documented here on this forum in the past, as written by scientists given the task of peer reviewing material.

I think you have a naive and idealistic view of the peer review process.

No I don't. I never said the process was perfect, because no process involving human beings ever is. However it's reliable, and far more reliable than apologetics.

Wortfish wrote:It works in some cases, where the reviewers have the time to reproduce the findings

Actually, I think you'll find the "hit rate" is better than 95%.

Wortfish wrote:but more often than not bad papers - even fraudulent ones - get published:

Ah, the "here's some rare instances of failure, that I'm going to inflate to dismiss the entire enterprise" trope we see all too often from creationists ...

Wortfish wrote:https://www.newscientist.com/article/dn7915-most-scientific-papers-are-probably-wrong/
https://www.spectator.co.uk/2016/10/how ... rent-true/

Item one: the New Scientist article's click-bait headline doesn't actually point to a fundamental problem with the scientific method, nor, as we read the article, with peer review, rather, it points to a problem with significance statistics, and moreover, the author of the paper in question is primarily concerned with the medical field (hence his paper being published in PLoS Medicine). Even more problematic for your apologetics, is that the article contains this telling response from a senior editor at Proceedings of the National Academy of Sciences of the USA, viz:

But Solomon Snyder, senior editor at the Proceedings of the National Academy of Sciences, and a neuroscientist at Johns Hopkins Medical School in Baltimore, US, says most working scientists understand the limitations of published research.

“When I read the literature, I’m not reading it to find proof like a textbook. I’m reading to get ideas. So even if something is wrong with the paper, if they have the kernel of a novel idea, that’s something to think about,” he says.

Indeed, one of the central principles of the scientific method, is that new data can overturn old results. See: the transition from Newton to Einstein, which I've covered in detail in the past. A second problem with your apologetics, is that the very fact that Ioannidis' paper was published in the first place, points to the willingness of scientists to tighten the rigour of their methods. Something that never happens in the world of apologetics.

In the meantime, when we delve into Ioannidis's paper in detail here, what do we find? Oh, that's right, we find this:

Ioannidis, 2005 wrote:Several methodologists have pointed out [9–11] that the high rate of nonreplication (lack of confirmation) of research discoveries is a consequence of the convenient, yet ill-founded strategy of claiming conclusive research findings solely on the basis of a single study assessed by formal statistical significance, typically for a p-value less than 0.05. Research is not most appropriately represented and summarized by p-values, but, unfortunately, there is a widespread notion that medical research articles should be interpreted based only on p-values.

Oh look. His focus was medical research articles, not articles across the whole of empirical science.

Furthermore, since this paper was published in 2005 (i.e., twelve years ago), scientists have taken a second look at statistical significance, and sought efforts from dedicated researchers in the field of statistics to tighten up the application of statistical significance. Indeed, you'll find there's a wealth of subsequent literature on the subject.

Item two: The Spectator isn't a scientific publication, it's a polemical right-wing political journal, several of whose own editorial board members, past and present, are right-wing politicians with an interest in science denial. On this basis alone, that link can be discarded.

Item three: the headline example of fradulent conduct in the third article was from economics, not empirical science, and indeed, I've examined the relevant papers covered by that article, which became the subject of an interesting thread over in the Economics section of the forums. Even worse, that article states the following:

Medicine and the social sciences are particularly prone to bias, because the observer (presumably a white-coated scientist) cannot so easily be completely removed from his or her subject.

Even more telling, most of the examples presented in that article, are from fields such as social psychology. The hard empirical sciences are, it seems, much less prone to the malaise.

Item four: who exposes the instances of bad science and the even less common instances of outright fraud? Oh, that's right, other scientists. Pedlars of religious apologetics are nowhere to be seen, until the scientists have done the hard work, then show up parasitically to misuse the results of the investigations.

So you can drop the duplicitous creationist trope, because those of us who paid attention in science class know it's another piece of blatant and duplicitous misrepresentation, one I've branded using the term "quantifier abuse" - namely, latching on to a small number of rare instances of a phenomenon, then asserting that the phenomenon in question is a universal problem for the discipline in question, tranforming a very restricted "there exists" into "for all" via apologetic sleight of hand.

Moving on ...

Wortfish wrote:A more useful criterion is whether the findings are validated in further research and the paper is cited accordingly. Unless this happens, scientific papers should only be regarded as tenatatively pointing to a possible conclusion that may be overturned.

Oh, you posture as being in a position to teach the rest of us this? Despite the fact that we learned about the provisional nature of scientific findings a lot earlier?

Ah, the smell of hubris ...

Wortfish wrote:

Actually, it doesn't even do that. It simply acts as a high pass filter for the functions that work.

Well, in that case, it merely lets the working functions continue into the next generation. It doesn't produce them.

Once again, read my previous post. I was referring to the entire evolutionary process. Don't add to the track record of duplicity that has already followed your postings here.

Wortfish wrote:

But I was, of course, referring to the evolutionary process in its entirety, including mutation and neutral drift, when presenting my remarks, as those who paid attention in science classes readily understand. Indeed, it won't take the diligent long to see me referring in the past here, to natural selection as a high-pass filter.

And Darwin was insistent that variation is observed to only modify already existing functions. He then speculated, as with his famous example of the swimbladder and the lung, that successive modifications over time could produce a new function or organ.

Oh actually, it turns out that this piece of "speculation" is now supported by molecular data. I have numerous papers on the development of lungs from Sarcopterygian swim bladders, several of which I've presented here in the past.

Plus, Darwin didn't have access to data on de novo gene instantiation. That is a modern development. I have numerous papers on that subject in the collection too.

Wortfish wrote:

And you think I didn't already know this? Ha ha ha ha ha. Read the above and weep.

It wasn't my first thought.

One wonders at this juncture what is being withheld here ...

Wortfish wrote:

Those early aircraft attempts I posted look a hell of a lot like blind experimentation. Indeed, quite a few of them were the result of efforts by people lacking any specialist understanding of fluid dynamics, even as the subject existed back in the 1900s or earlier. For that matter, the advent of successful aircraft, was one of the developments propelling a more modern understanding of that discipline. Do you think anyone with even a circa 1900s understanding of fluid dynamics, would have tried using exposed paddle wheels as a propulsion system for an aircraft?

Do you have any example of how engineering is practised today using no thought process or foresight whatsoever?

Ah, more misrepresentation. I never claimed in my above exposition, that the individuals in question did not apply thought to the matter, merely that they applied incorrect thought as a result of knowledge gaps. But keep demonstrating how the process of apologetics twists the statements of others out of recognition.

Wortfish wrote:

However, Otto Lilienthal, who set out from the beginning to understand aerodynamic concepts, enjoyed successes with towed gliders and prototype hang gliders nearly two decades before the Wright Brothers produced a working powered aircraft. His gliders, thankfully thoroughly documented, start to look like an evolutionary series when placed in chronological order. The Otto Lilienthal Museum contains both extensive original documentation from Lilienthal's own pen, and scale model replicas thereof.

Well, that's nice to know. Some technological leaps may have been accidental - I can think of beer as a case in which bread and yeast fermented with water to give alcohol. That wasn't designed or planned. However, I seriously doubt that the steam engine - the machine that transformed industry - just came about by a process of mindlessly experimenting with steam and pistons.

And once again, this apologetic misrepresentation of my exposition is precisely that.

Quite simply, the notion I have presented here, one understood without such misrepresentation by everyone else, is that with an infant technology, key pieces of knowledge are, by definition, absent at the beginning of the enterprise, and await discovery. The trouble being, of course, that discovery thereof is made all the more difficult, if clues pointing in the right direction are also absent, which is sometimes the case. Those early aircraft experiments point to [1] absence of key pieces of knowledge, [2] a shortage of clues available to those responsible for the documented failures, and [3] insufficient specialist knowledge on the part of the same persons, that might have pointed them in a better direction. I have no doubt whatsoever that they had ideas from the start, and a determination to test those ideas empirically. The problem is that the ideas in question were wrong, the evidence for this being the dismal failure of their artefacts.

As for steam engines, well Heron of Alexandria constructed a toy model that could have produced a small amount of mechanical power around 50 CE, but it wasn't especially practical. Likewise, prior to the Industrial revolution, there are a number of early attempts to produce steam engines that enjoyed a chequered degree of success. An early steam turbine, used as a roasting jack, was described by an Ottoman polymath, one Taqi al-Din, back in 1551. Likewise, Thomas Savery's steam pump from 1698 didn't have pistons, and indeed had no moving parts other than taps. Had it worked, it would have been quite an achievement, but unfortunately, it had serious flaws. Meanwhile, the Frenchman Denis Papin, having successfully constructed a pressure cooker, and witnessed first hand the power of steam under pressure, developed the first prototype steam engine with a piston in 1690, and was given no credit for his insight when he came to London, despite having, in 1704, built a modestly successful steam-powered boat (indeed, Papin's vessel employed a rudimentary version of a steam turbine).

Once again, the actual history is a lot more complicated.

Wortfish wrote:

Ahem, I'll point you at Astyanax mexicanus and other blind cave fishes. Which readily discarded functioning eyes the moment they ceased to be of use. In the case of A. mexicanus, however, eye-loss populations of cave dwelling members of the species, upon finding themselves in a karst window, reacquired functional eyes. I've covered the scientific papers in some detail in the past. In the meantime, you can fire up this scientific paper, go to page 8572, and see the step by step stages of building an eye over time from simpler antecedent structures.

Well, that kind of implies that the organism itself is able to switch off and then switch back on its own visual apparatus.

No it doesn't, as you would know if you bothered to read the papers in question. This wasn't an "act of will" on the part of the fish, rather, it was the consequence of one set of mutations affecting the Pax6 gene (among others), resulting in loss of functional eyes that wasn't a hindrance in a totally dark cave, followed by the karst window fishes acquiring other mutations in Pax6 that restored eye functionality, and became useful in that environment.

Wortfish wrote:There is a purpose or intent about this.

Poppycock. See above.

Wortfish wrote:In fact, the field of "niche construction", whereby organisms select their own environment and even variations, brings purpose back into the evolutionary process as it makes organisms active subject and not passive objects.

No it doesn't. Because what really happens is niche migration. Namely, organisms find something new to eat. When that new food item is accompanied by few or no competitors, this is frequently the trigger for adaptive radiation and speciation. The Cichlid literature is particualrly informative here.

Furthermore, evolutionary biology doesn't view organisms as "passive objects". This is your fabrication.

Wortfish wrote:

And those signatures are what, precisely? Provide in detail, a breakdown of the differences between stones shaped by natural erosion, and stones shaped by human activity. I'll have fun watching the palaeontologists gather round and observe.

That's what palaentologists do. They look for evidence of design in the way stones have been altered or whether fires have been deliberately started by design by primitive humans. It is not an exact science but it is an inferential science with methods.

Details? Care to provide some?

Wortfish wrote:http://rstb.royalsocietypublishing.org/content/371/1696/20150164
http://www.smithsonianmag.com/science-n ... -55335180/

The first of those articles isn't a detailed account of tool use and manufacture, rather a history of interaction with fire. The second is merely an overview of the history of tool use and manufacture, and again does not cover details. So, once again, what distinctive features differentiate a rock shaped by natural forces, and a rock shaped by humans?

Wortfish wrote:

Well that's the assertion being tested here, isn't it? Namely, that entities pursuing a goal with intent, purportedly produce observational data that are distinguishable from the data generated by natural processes. This is the central creationist assertion that I'm asking you to address. If this assertion is true, then it should be possible to state the nature of those distinguishing features, both by reference to example and via deduction from first principles. Can you do this?

It is a qualitative judgment.

Actually, if those distinguishing features are present, as asserted, then it should be possible to place them in a quantitative framework. But even in the absence of this principle, I'm still waiting for details.

Wortfish wrote:Design aims at perfection, optimal performance and efficiency

This assertion in itself is highly debatable, and again points more to your ideological predilections than to the facts. In general, the first task that is pursued by humans is "can we make something that works?" The question "can we make it work better?" arises later. See those early aircraft again.

Wortfish wrote:whereas non-design, if it works at all, does not.

Hmm, so you don't think natural selection, acting as a high-pass filter, acts to improve function, despite implying earlier that this was actually so? Interesting the twists and turns that apologetics takes ...

Wortfish wrote:That is how I would distinguish between the two.

This is vague to the point of being nebulous. Detail again?

Wortfish wrote:Some features in biology look very much like they have been designed by an intelligence. Indeed, Richard Dawkins accepts that this is the distinctive characteristic of living organisms.

The old adage "appearances are deceptive" springs to mind here, and indeed I gather Dawkins goes on to say as much, with considerable elaboration thereupon.

Wortfish wrote:

"Biology is the study of complicated things that have the appearance of having been designed with a purpose."

https://www.brainyquote.com/quotes/quot ... 26696.html

That is an isolated quote taken from The Blind Watchmaker, with which Dawkins introduces an entire chapter devoted to demonstrating that the appearance cited in that quote is woefully deceptive. Later on in the chapter, the following is illustrative of his actual views:

Richard Dawkins, The Blind Watchmaker wrote:Paley's argument is made with passionate sincerity and is informed by the best biological scholarship of his day, but it is wrong, gloriously and utterly wrong. The analogy between telescope and eye, between watch and living organism, is false. All appearances to the contrary, the only watchmaker in nature is the blind forces of physics, albeit deployed in a very special way. A true watchmaker has foresight: he designs his cogs and springs, and plans their interconnections, with a future purpose in his mind's eye. Natural selection, the blind, unconscious, automatic process which Darwin discovered, and which we now know is the explanation for the existence and apparently purposeful form of all life, has no purpose in mind. It has no mind and no mind's eye. It does not plan for the future. It has no vision, no foresight, no sight at all. If it can be said to play the role of watchmaker in nature, it is the blind watchmaker.

I shall explain all this, and much else besides. But one thing I shall not do is belittle the wonder of the living 'watches' that so inspired Paley. On the contrary, I shall try to illustrate my feeling that here Paley could have gone even further. When it comes to feeling awe over living 'watches' I yield to nobody. I feel more in common with the Reverend William Paley than I do with the distinguished modern philosopher, a well-known atheist, with whom I once discussed the matter at dinner. I said that I could not imagine being an atheist at any time before 1859, when Darwin's Origin of Species was published. 'What about Hume?', replied the philosopher. 'How did Hume explain the organized complexity of the living world?', I asked. 'He didn't', said the philosopher. 'Why does it need any special explanation?'

Paley knew that it needed a special explanation; Darwin knew it, and I suspect that in his heart of hearts my philosopher companion knew it too. In any case it will be my business to show it here. As for David Hume himself, it is sometimes said that that great Scottish philosopher disposed of the Argument from Design a century before Darwin. But what Hume did was criticize the logic of using apparent design in nature as positive evidence for the existence of a God. He did not offer any alternative explanation for apparent design, but left the question open. An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist. I like to think that Hume would agree, but some of his writings suggest that he underestimated the complexity and beauty of biological design. The boy naturalist Charles Darwin could have shown him a thing or two about that, but Hume had been dead 40 years when Darwin enrolled in Hume's university of Edinburgh.

I don't propose to post all 18 pages of that chapter to reinforce the point, but the above is a suitably illustrative excerpt.

Wortfish wrote:

This assumes in advance that the process either possesses goal-oriented sentience, or was produced by one. We have zero data telling us this.

Illusion implies that something intelligent is illuding us.

Ahem, what "intelligence" is responsible for mirage illusions? Er, none. It's light refraction.