This is a companion discussion topic for the original entry at https://biologos.org/blogs/jim-stump-faith-and-science-seeking-understanding/reviewing-creatorgate-how-science-is-like-soccer
the id guys actually do science. a scientific theory its a theory that we can test. and we indeed can test concept like ic to check if its real or not.
A scientific theory is a theory that we can test using the scientific method.
and the scientific method base about claims that we can tests
6 posts were split to a new topic: The “design” of the eye
The "design" of the eye
Thankyou for addressing this topic. It is interesting how creation.com had an article on something like this:
Controversy is raging after a peer-reviewed open-access scientific journal, PLOS ONE, published a paper1 recently by a team of four Chinese researchers (three in China, one in Massachusetts).2 The paper dealt with everyday topics such as how human hands grasp objects, and showed these actions that we take for granted require “complex biomechanical architecture”. But this would hardly have been controversial if not for its ‘unfortunate’ use of some extremely taboo language: the researchers in multiple places referred to the Creator. E.g., the Abstract states:
The explicit functional link indicates that the biomechanical characteristic of tendinous connective architecture between muscles and articulations is the proper design by the Creator to perform a multitude of daily tasks in a comfortable way.1
The Introduction includes:
Thus, hand coordination affords humans the ability to flexibly and comfortably control the complex structure to perform numerous tasks. Hand coordination should indicate the mystery of the Creator’s invention.1 creation.com/hand-design-peer-review
Scientists are apparently not permitted to have certain opinions or perspectives or deductions, and must also apparently use a certain type of politically correct language. Amazing. And you thought that the thought police didn’t exist in science.
It is one thing to disagree with their statement or their perspective. It is another thing entirely to prevent their expression without any scientific counter evidence whatsoever.
We can be certain that what many scientists mean when they say something is “uniquely evolved” or “especially suited” or “mysteriously adapted”, is that they are possibly referring to “marvelously designed”.
> You also talk about hand coordination as evidence of “the mystery of the Creator’s invention.” What mystery is that? Is there a mystery how evolution by natural selection could produce the coordination in question?1Ming-Jin Liu, Cai-Hua Xiong , Le Xiong, Xiao-Lin Huang, Biomechanical characteristics of hand coordination in grasping activities of daily living, PLOS ONE, 5 January 2016 | doi:10.1371/journal.pone.0146193. PLOS = Public Library of Science.
No problem with them asking the question… but are they citing the evidence of this development?
And if they had originally used the word “nature” instead of “creator”, would this article have received the approbation it did. Not likely. As long as nature is god, it is okay.
> It should be noted that the response below, by senior editor Jim Stump, deals with the hypothetical scenario of a scientist invoking a supernatural creator in lieu of a natural explanation for something, which is not exactly what happened in #creatorgate, but is still worth discussing because it sums up what made this article controversial in the first place. - See more at: http://biologos.org/blogs/jim-stump-faith-and-science-seeking-understanding/reviewing-creatorgate-how-science-is-like-soccer#sthash.SBMv7526.dpuf
"…invoking a supernatural creator in lieu of a natural explanation for something, which is not exactly what happenedemphasized text…"
It seems rather beside the point to discuss something that never happened. Doesn’t it seem like a bit of bait and switch? If they were merely using their words as an excuse for ignoring evidence, or information, or doing work, perhaps the critique would be legitimate. But their words were part of a summary conclusion of their work. They understood that our grasp of the workings of the hand and its development is a mystery. So be it. They obviously didn’t think it couldn’t be explained in many ways, because that is what they did.
The critics did not object to the work they did, but only to the language they used. Shame on them for such a narrow minded view of science.
Arguing about the “rules of the game” is beside the point. This is not about the rules of science, but about the expression of scientists.
Really? I’m still waiting for how anyone can PROVE design?
John, I think you missed the point of Jim’s argument. It has nothing to do with being permitted to have certain opinions or perspectives and certainly nothing whatever to do with political correctness.
Let’s take an example - me. I am a devout Christian, totally committed to my belief in Jesus Christ, and the fact that God created the universe. And I express that belief in Church, on facebook in the group Celebrating Creation by Natural Selection, in articles I submit to Christian based organizations devoted to the interactions of science and faith like the ASA and Biologos. But I would never include the fact that I believe in a creator in a scientific paper (In fact I am preparing to send one to PLOS 1 very soon). Why not?
Because of what Jim said. There are many rules that must be followed to get a paper published in the scientific literature. Not mentioning a creator is not one of them. But the rule that is violated by mentioning one;s belief in a Creator is that any expression of belief or opinion, that is not immediately backed up by the facts presented in the paper is not allowed.
I have reviewed countless papers, and published over 200 of them. I have both written and received reviews with comments like “The author claims that X is real, but there is no support for this claim in the data presented” X could be the activation of an enzyme, or my belief in Christ as my redeemer. Either way, if I have not presented data to support the statement, that language, or the entire paper will be rejected.
This is not censorship, it is a vital rule, established over more than a century of scientific scholarship. It is enforced by peer review (which was really what the failure was in the PLOS 1 case) and without that rule, the scientific literature would be flooded with nonsense like the ravings of nutrition quacks, alien watchers, and conspiracy theorists. The publication of Wakefield’s fraudulent study on vaccination has cost lives and set back public health for years. That was a failure of the system for not being tough enough.
So, as a Christian who is devoted to the faith, and to spreading the Gospel everywhere, I will state quite strongly that any relaxation of the strict rules of what can be published in a scientific paper would be a disaster for science, truth and the cause of Christ as well.
While I would agree with the thrust of your comments, I would add the following. Stating that a “creator” may have caused the aspects of the hand they are discussing, is (in the scientific sense) opinion and belief, and thus may need further elaboration, and on that basis, a reviewer should ask for further comment, to be satisfied the authors can sustain their opinion. Yet I have come across many papers where terms such as “natural selection”, or “evolution” are used in a similar sense, as justification, or expressions of belief, and no-one in the bio-community is bothered, nor are authors asked to justify scientifically their belief.
This lopsided approach has convinced me that ideology is embedded in the outlook of the biosciences.
Hi G -
Hope you are doing well this Friday! Unlike you and many other forum participants, I am not a practicing/publishing scientist. I wonder whether your evidentiary standard might be too high for the biology papers, though.
Compare them to papers in physics, say. If someone publishes a paper that gives a more precise measurement of the perihelion shift of Mercury, they might discuss how it is explained by relativity. We wouldn’t expect the authors to present a summary of all the evidence for relativity; it has already been established in the scientific discipline, it is widely accepted, and it provides explanatory power for this particular observation. There would perhaps be other theories that could account for the shift, but they don’t get explored; relativity has already won the day, and it fits the observation being reported.
Likewise in the fields of biology. A particular observation about chromosome 2 in homo sapiens sapiens would be woefully insufficient, by itself, to build the case for evolution. But if you are a biologist submitting a paper, you don’t feel the need to build that case. The case for evolution has already been built and confirmed by the observations of generations of biologists. As the author of a biology paper, you can simply refer to the paradigmatic theory in your field and move on.
This is not to say that overreach never occurs in a biology paper. I’m sure your critique is spot on for many published works. Is it possible you might have overgeneralized, though?
May the Lord continue to bless you with His wisdom and strength…
Your thoughtful response is spot on, and under “ordinary” circumstances, we would be in total agreement. However (it seems there is always a however), our discussions are not confined to one or two branches of science. Evolutionary biology is extended into aspects of religious doctrine, origins and (by some) nature of humanity, and a plethora of beliefs and outlooks. I have constantly maintained a view that if biologist confined their remarks to their current paradigm, all other scientists (including myself) would be happy to leave them at their task - I am also confident that biology would advance as a result. But this is not the case - evolutionary biology has become the mainstay of materialists, Dawkins and Co., who insist it will overthrow faith, others want a theology that is evolutionary in its outlook (EC, TE) and so on. In this contest, I think you may agree with me, that the claims are extraordinary, and the bar to dealing with such claims must be higher than you and I may ordinarily consider appropriate.
I have to smile on this one - I have published a few papers on an aspect of catalysis that is novel, and I have been reminded by competent reviewers of the need to build a case - this is in spite of the fact the theory of catalysis is very well established and has a mountain of experimental and theoretical (and Nobel Prizes) work in support.
We must accept the requirements of science, which can be rather stringent at times. I have at times tried to illustrate my point by showing that some papers would not change in content or meaning one bit, if we removed the terms “evolution” and “natural selection” - simply to show these terms are often used as a worldview, without any scientific relevance to these papers - if this is the case, what is different to using terms such as “creator”?
Thank you for your kind remarks and I hope they are returned many fold - yes, often in these exchanges we oversimplify and overgeneralise at times. Such is the world of blogs.
I found this statement to be very interesting. What you are suggesting, in effect, amounts to a wholesale inversion of the peer review process. You seem to be saying that the author can throw in whatever opinion they’d like and the peer reviewer has no reason to reject the paper or the opinion unless they can marshal evidence against that opinion. In effect (though obviously this was not your intention), a taxonomy paper could construct a phylogenetic tree for unicorns based on morphological features, and it would be up to the editors to establish that unicorns didn’t exist if they wanted to reject the paper. It puts the onus on the wrong side and in a way that would be disastrous for almost any field of thought or study. This inversion seems massively problematic to me.
I think that this looks like a fallback position (in case it really isn’t ok to invoke something that hasn’t been scientifically established). Essentially, the argument is; but other scientists do exactly the same thing, but with “nature” in the place of “a creator”, so there is obviously a double standard in play here. Sure, if these two terms were equivalent. The only way they can be made equivalent is through the observation that in the minds of some, nature and God are about the same thing. While true, this is entirely beside the point. There are also people who think that oak trees are dryads, but this is obviously not the proper referent for a scientific paper discussing oak trees. In a scientific paper, the meaning of “nature” is limited to “the natural world”, which is not some arcane divinity presiding over our forests and fields, but simply the world of matter and energy that is the proper study of science and all of the known processes at work in this context. If “nature did it”, then what is being said is usually that known (and generally obvious) natural processes produced the results, and anything else is probably to introduce more into the expression that it is actually meant to contain. If nature was overtly called a divinity, you would be correct, but as the only appropriate subject of study for the sciences, it seems to be a pretty big stretch to insist that it should be scientifically proven to exist before invoking it in a scientific paper;-).
You frame the whole situation as a sinister exercise perpetrated by the Orwellian thought police, and although I think I understand why you see it in this way, I can’t see how this holds up, and I think the points made by Sy above serve as the best antidote for this misunderstanding. Ultimately, I think your (and Ken Ham’s) outrage about the secular bias that this incident highlights make sense in a way, but that it is partially based on a misunderstanding. The inclusion of a term like “creator” obviously had no place simply because it was unsupported by a single argument or reference, and it did not refer to anything that is the proper subject of study for, or one of the generally accepted premises of the sciences. Period. Obviously, at a minimum, the term should have been either removed, or supported by references and arguments (which given the limited scope of the paper, is rather a far-fetched proposition). That said, I think the outrage can be appropriately directed towards many of the online reactions (and possibly towards the overreaction of retracting instead of just correcting the paper, though this is probably just a strategy for mitigating the fallout) that are clearly fueled by an anti-Theistic bias rather than a reasoned consideration of whether unsupported terminology was appropriate in the context of the paper.
Hi G -
I do appreciate your sharing your experience as a scientist. Surely there must be some foundational paradigms you can cite in a chemistry paper, though? Could you say that water is composed of molecules, molecules are composed of atoms, atoms have a nucleus and electron cloud, the s orbital contains no more than 2 electrons, without having to cite experimental observations?
It’s also worth noting the different standards for research papers and books. When Dawkins expressed his religious beliefs about ultimate reality, it was typically in his books rather than research papers, if I am not mistaken. A lot of what he claimed in his books would not have passed peer review, I suspect.
Again, as a non-scientist I could be wrong, so I would welcome more data from folks like you, @Sy_Garte and @DennisVenema (and many others) who know the world of “publish or perish” far better than I ever could.
The "design" of the eye
I have referred to an example related to heterogeneous catalysis to illustrate my point - discussing “foundational paradigms” is an awfully difficult concept for any research paper that I have written or reviewed. This is where discussions on evolution come unstuck. For example, one person seemed to think the periodic table of elements is such an example of a foundational paradigm, and used this as an analogy for Darwinian evolution. That discussion quickly became irrational imo.
If I were to give a valid example, such a research paper would need to deal with the nature of the chemical bond, what we mean by molecules, and from that present a theory that deals with every aspect of chemistry. Such a paper is rarely (more likely never) provided, but instead theoretical treatments of particular bonds and electron distribution within specific molecules may be discussed using ab initio methods (QM). Stating that s orbital contain 2 electrons is trivial and using such in a paper would be considered humorous.
Regarding standards, I remind all of us that non-scientists have little trouble arguing from the “scientific method” and various versions of this - if they generalise in this way, than they must accept the standards of the Physical Sciences. If they wish evolutionary biology to be exempt from such standards, they must say so, or avoid inferring their working within such a standard. This is a horrific aspect of discussions on BioLogos (I do not visit other sites embroiled in the ND controversy). People have little trouble claiming Darwin is like Newton, ND is like quantum mechanics, and other nonsense.
It is not so much “publish or perish” as far s I understand it, but rather publish and see the response to your research. The angst is found in ways some use to obtain funding for their research.
My comment has inevitably focussed on the mixture of biological science and ideology (now mixed with theology). This is where people err as self appointed “theologians” make such free and easy comments about science and faith, The subject matter is profound and requires a much better appreciation of both science and theology from all of us (including myself).
I do understand that most people not working in science really have no idea of what it means to write, review and publish a scientific paper. Why should they? Scientists (including all of us) learn the rules and customs from our mentors and advisors in grad school, and then by trial and rejection. I suppose it might be of some interest to summarize some of that as it relates to your comment, and the issue of the PLOS paper.
The style of a scientific paper is generally very constrained; passive tense is encouraged (the opposite of books) so that “In order to test this hypothesis, an experiment was designed…”. is the rule.
Introductions are short (a few paragraphs) summaries of what the paper is about, including some mention of what came before, usually just a line with lots of references. “Previous workers (Smith 2012, Jones et al. 2014) have found that standard evolutionary models do not fit the kinetic data…” and so on. As GJDS said, basic stuff like what is evolution, or enzyme kinetics is not allowed. The reader is assumed to be a trained scientist in the field or a related field to the subject of the paper (Also not true for books).
It is unheard of to make a new claim without any reference to previous work. Even breakthrough revolutionary works of genius must refer to previous work in the area. (There is also a practical reason to include lots of references. The odds are high that some of the people being referenced will be reviewers, and nothing makes a reviewer more cranky than not seeing his own work referenced. Yes, I speak from experience).
The Introduction is generally followed by a Methods section which goes into varying amounts of depth and detail depending on the field. When PCR was a new technique I used to present all the PCR conditions and primer sequences. Now people just say “by PCR”.
The Results section is required to be crisp, to the point, and limited to basics. No flowery language is allowed. A typical sentence might read “We found no evidence for homeostasis (Figure 1).” The heart of the results section is the data, presented in figures and tables. Some results sections can be incredibly dense, with a huge amount of information crammed into one sentence. Here is an example from a paper Im reading now by Andreas Wagner
Figure 5 shows that a genotype’s vertex degree and its number of latent phenotypes are weakly,but significantly positively correlated (Spearman’s r = 0.13, p < 1.2 × 10−41), indicating that mutationally robust circuits have an increased capacity for exaptation
Then comes the fun part, the Discussion. Here the authors are allowed a bit more leeway in terms of eloquence and even some degree of deeper thought. (The creator word was used in the Discussion). Here, (and not in the Results section) the meaning of the results can be discussed, almost always in the context of what everyone else has found, both in agreement and in contrast with the work presented. Thoroughness is key. Leaving out some key work by other groups is often fatal.
The entire approach is decidedly low key. A paper that purports to have “made a significant and groundbreaking discovery that will change the nature of how we think about” would not even get sent out for review. It aint the internet. The use of qualifiers like “could” or “might explain” or “is consistent with” or “lends support to the idea that” are very common. Phrases like “we have proven that” simply do not appear. (With the exception of mathematics, and some rare physics papers).
As you said Chris, none of this applies to books. I felt a huge sense of freedom while writing my first mass market book, since I realised I could say almost whatever I wanted to (I still included lots of graphs, which turned out to be a mistake for sales, but thats another discussion).
Is this the best way for scientists to communicate? I dont know. The style of 19 century papers was completely different. They were long, and long winded, with philosophical musings, and off topic tangents, all now forbidden. Some people have said we need to reform the way we write papers. Maybe, but I will bet it wont happen.
@GJDS - I think I may have been imprecise in when I was asked:
I did not mean that a chemist would write a research paper today that would try to prove these statements. What I meant was: in the context of discussing research on some other chemistry topic that is somehow related to well-accepted concepts [not necessarily my specific examples], could the well-accepted concepts be mentioned without having to marshal evidence for them?
Based on your response, it seems to me that a chemist could refer to the general theory of chemical bonds and/or quantum mechanics, in order to discuss a particular bond that is the subject of research. And the chemist would not need to provide evidence for QM or the general theory of chemical bonds, because those concepts are well-accepted. Am I understanding this correctly?
I would agree that biologists such as Dawkins have, in their books, have clearly overstepped the bounds of what science can infer when they have opined upon religion and philosophy. On the other hand, I have read a bit of primary literature on the topic of evolution, and when I have, it seems not to have contained any of the grandiose Dawkinsian claims. Not being a biologist, I would not want to claim that the primary literature never contains such claims. However, I am wondering whether you might be conflating the sweeping overgeneralizations of tertiary literature (and discussion forums) with the more careful discussions present in the primary literature.
Take care, my friend!
BTW: when “Dawkinsian” becomes the 2016 Word of the Year, you read it here first!
Yes, your statement can be understood generally as correct - the wording is awkward however. If the paper dealt with some aspect of chemical bonding, the author(s) must discuss QM as part of their discussion. Sy has made the structure of scientific papers very clear. QM (or any general theory) has been discussed in many, many, papers, so the authors must locate the relevant papers that cover the theoretical aspects of their research, and show how they are adding or clarifying something within that aspect of QM treatment of chemical bonds. This what is meant by well accepted. I would not publish a paper that states “because QM is well accepted, my results are therefore correct”, or “these results are so because of QM…” or similar statements.
QM and chemical bonding theories are quantified and require a considerable understanding of the maths - thus data must be dealt with in a quantitative manner, as must the theoretical treatment. It is here that papers dealing with some aspects of biological sciences fall short - they simply use phrases such as “because of evolution…” or in discussing their data, they simply say this is evolution. Such discussions are foreign to me … I am not saying they are false, but pointing out that much of this stuff is semantics, and this semantic treatment goes back to the original formulation of evolution as variation and natural selection. Variation can be observed and is a non- starter, while natural selection is central to the outlook, and has never been grounded in a quantitative manner, nor derived from first principles. My remarks are non-controversial and are restated in various ways by evolutionists themselves.
So I am making a valid criticism, not in the context of how biologists work, but what is used in discussions of theology (and by atheists for materialism). When semantics are used in this way, I regard such as ideology - I have mentioned a small amount of primary literature (in past posts) simply to make my point on how “evolution” is often used by some. Generalisations can often stem from primary sources that can easily be manipulated.
I do not think I can add to these type of remarks in this forum, so I suggest that we leave this subject - if you wish to discuss something more specific and theologically relevant, I will be happy to continue this conversation.
Hi G- I appreciate the deeper explaination. It helps me as a non-scientist to understand the point you are making.
It also seems that you are not fond of the scarcity of mathematics in much biology theorizing. I wonder if that would be the result of the complexity and stochasticity of biological processes; i.e., the processes can be described using rules of thumb and computational logic. Biological inferences, however strongly they may be drawn, are difficult to describe numerically because the process under study (say, the evolution of cetacean appendages) was occurring in a context that is, to some extent, not replicable. I am sure the biologists who participate on the Biologos forum could provide a more rigorous description of how biologists use inference, and I welcome any clarification, elucidation and correction they might care to offer.
Perhaps I am not so averse to biology because I work in the field of software development, where rules of thumb and computational logic reign supreme.