Hossjer: Using statistical methods to model the fine-tuning of molecular machines and systems

Fine-tuning has received much attention in physics, and it states that the fundamental constants of physics are finely tuned to precise values for a rich chemistry and life permittance. It has not yet been applied in a broad manner to molecular biology. However, in this paper we argue that biological systems present fine-tuning at different levels, e.g. functional proteins, complex biochemical machines in living cells, and cellular networks. This paper describes molecular fine-tuning, how it can be used in biology, and how it challenges conventional Darwinian thinking. We also discuss the statistical methods underpinning fine-tuning and present a framework for such analysis.

Dembski, Axe, and Behe come up, and the paper includes essentially a review of just about all ID arguments we’ve heard. This is a secular journal, but does make me wonder about who the editor was and who reviewed it. It is hard to imagine this paper surviving an unbiased review.

It seems a key question in analyzing this paper is determining the extent to which their argument depends on, for example, Axe’s work. The strongest case would not have such dependencies, and would thereby avoid inheriting the criticism of prior work. I don’t see much data.

The final sentence of the paper is interesting though:

Yet researchers have more work to do in order to establish fine-tuning as a sustainable and fully testable scientific hypothesis, and ultimately a Design Science .

Editor’s Disclaimer

The Journal of Theoretical Biology and its co-Chief Editors do not endorse in any way the ideology of nor reasoning behind the concept of intelligent design. Since the publication of the paper it has now become evident that the authors are connected to a creationist group (although their addresses are given on the paper as departments in bona fide universities). We were unaware of this fact while the paper was being reviewed. Moreover, the keywords “intelligent design” were added by the authors after the review process during the proofing stage and we were unaware of this action by the authors. We have removed these from the online version of this paper. We believe that intelligent design is not in any way a suitable topic for the Journal of Theoretical Biology.

Disclaimer - ScienceDirect (paywalled)

Rebuttal Paper Published

Large sample spaces do not imply biological systems are ‘fine-tuned’

We write to rebut the conclusions of a recently published paper in the Journal of Theoretical Biology (Thorvaldsen and Hössjer, 2020). The central claim of this paper is that because biological systems are complex then they must be fine-tuned. This inference is flawed and is not supported by the evidence.

What does this paper contribute to our understanding of theoretical biology? The primary claim of Thorvaldsen and Hössjer is that protein complexes, molecular motors, and biological networks are not random. This is true – in a mathematical sense - but is not a new discovery. What they claim to be novel is the conclusion that the existence of these specific systems amongst the space of all possible systems is so rare as to only possibly exist by ‘fine-tuning’ – a proxy for intelligent design. That components of living systems - or systems themselves - are exceedingly rare does not suggest agency or intent. Furthermore, irreducible complexity ignores the idea that evolution and natural selection act on a pool of variation: any number of individuals within the pool will not pass on their genes because their specific complement of protein complexes and cellular networks do not accomplish the necessary functions for life to continue. Hence, neither fine-tuning nor intelligent design is required when sample spaces are viewed through the lens of evolutionary dynamics.

Notably, the authors of this paper list “Intelligent Design” as a keyword and repeatedly return to the idea of irreducible complexity, a hallmark of creationism. These ideas have been repeatedly debunked in the past. In the words of Carl Sagan: “extraordinary claims require extraordinary evidence”, a threshold that is not met in this paper.

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Covered at ENV here:

The article explicitly cites work by Discovery Institute Fellows such as Stephen Meyer, Günter Bechly, Ann Gauger, Douglas Axe, and Robert J. Marks. The article is co-authored by Steinar Thorvaldsen and Ola Hössjer. Hössjer is a professor of mathematical statistics at Stockholm University who is favorable to intelligent design.

This is a big deal for the mainstreaming of ID.

The Journal of Theoretical Biology is a top peer-reviewed science journal. According to CiteScore, it is the 25th most cited journal in the area of general agriculture and biological sciences, and it is in the top 12 percent of all journals in that field.

The article by Thorvaldsen and Hössjer appeared online in June. But we didn’t want to speak about it publicly until after its “official” publication date, because we knew that once Darwinists found out, they would try to have the article cancelled.

Seems like they are using the Irreducible Complexity argument, calling it endearingly a Behe-system.

A Behe-system of irreducible complexity was mentioned in Section 3. It is composed of several well-matched, interacting modules that contribute to the basic function, wherein the removal of any one of the modules causes the system to effectively cease functioning.

But Which Irreducible Complexity? Seems to be IC1:

However, Behe backed off this definition of IC, noting:

While thinking of Keith Robison’s scenario, I was struck that irreducible complexity could be better formulated in evolutionary terms by focusing on a proposed pathway , and on whether each step that would be necessary to build a certain system using that pathway was selected or unselected.
In Defense of the Irreducibility of the Blood Clotting Cascade | Discovery Institute

To which he proposed, IC2:

That’s notable, then, that this paper is not using Behe’s most up to date version of IC, and doesn’t recognize that Behe concedes that IC-systems can evolve.

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This is the same Ola Hossjer who published a paper with Ann Gauger last year on the “First Couple” Adam and Eve in the DI’s pretend science journal BIO-Complexity. I can’t imagine this paper is any better with its constant references to “Darwinian evolution” and “Darwinian thinking” and its many references back to other BIO-Complexity articles. I can only suppose this paper made it through peer review because the referees were statisticians and not familiar with evolutionary biology.

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I’m off for a weekend getaway, but I’ll try to read it when I can.

Just added the editorial disclaimer and the rebuttal that was published. I’m curious what @sfmatheson thinks about the editor’s note.

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Most of the editorial disclaimer seems to be about whether the editors knew that the authors are creationists. I speak only for myself when I say that I don’t care about that. Scholarly papers ought not be judged on the reputation or associations of the authors, and that’s one reason why double-blind peer review is being actively discussed among biologists and other scientists. I do think it is reasonable (but should be unnecessary) for editors to disclaim creationism and essentially everything that the modern ID movement is about.

What caught my eye, though, is the claim that the authors changed the paper after peer review. This, to me, is potentially very serious and it would (at our journal) precipitate an investigation that could lead to rejection (before publication) of a paper. It has never happened at Cell Reports, as far as I know.

I have not read the paper, but the rebuttal they published alongside it suggests that it is a poor reflection on the journal. If the authors did indeed make claims about “fine-tuning” based on rarity of biological outcomes, then that should not have gotten past peer review at a respectable scholarly journal.

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True, but that was just the list of key words, and that change was rolled back. The substance of the paper is all ID, but that is not in the abstract. I don’t think the editors are claiming there were post review changes to the main text. It seems the editor may not have actually read the article before sending it out for review.

Ah, good point, I read the disclaimer too quickly. You are right that this kind of post-review change is less of an ethical problem. It does suggest intent to deceive but simply deleting it is a reasonable response.

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There is a really interesting paragraph here that seeks to connect @Agauger and Sanford/Carter’s work on Adam and Eve to intellilgent design:

We believe the model selection approach is very promising for future fine-tuning research. It can be used, for instance, when deciding whether the diversity of life is best explained by Darwinian macroevolution (M2) or a design-inspired model (M1). Examples of design-inspired models are the Dependency Graph of Winston Ewert (2018), and a forest of microevolutionary family trees, where the species within each family tree descend from a designed common ancestral population (Tan, 2015, Tan, 2016). One may also study the more restricted problem of human/chimp ancestry, and compare a model M2 with common ancestry of the two species, with a unique origin model M1, according to which each species is founded by one single couple (Sanford and Carter, 2014, Hössjer et al., 2016a, Hössjer et al., 2016b, Carter et al., 2018, Hössjer and Gauger, 2019).

That’s an interesting move on several levels. A single couple origin does not actually imply intelligent design by itself. It is also interesting to see YEC models offered up explicitly as ID (Tan, Sanford, Carter). Poor Nathaniel Jeanson. His YEC Adam and Eve model not referenced!

The attempt to draw on the idea of physical “fine tuning” of the fundamental constants, as if that is at all analogous to the specific outcomes of an evolutionary process, doesn’t make any sense. I find that the way they try to draw parallels between them in the paper is essentially word salad.

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It’s ludicrous and a huge embarrassment to the journal. That’s all it is.

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Yes, but that’s the first time I’ve seen that connection made by ID proponents about ID. That would be notable even if they just put this in ENV.

This seems wrong on a few levels, including that the authors are creationists who are leveraging “ID” (this is beyond commonplace) and that the hilarious “descend from a designed common ancestor” is in fact beyond commonplace in ID “thought.” This isn’t news. The ID movement is 5 or 6 people thinking about design and 10 million who need magic to make their world work.

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See the Panda’s Thumb piece by Matt Young:

It appears that the article has slipped past the editors, and they are trying to do damage control. I cannot fault the editors: the authors had legitimate university affiliations, and they have no obligation to state all the organizations they belong to, unless they perceive a conflict of interest. I doubt that the editor-in-chief of any journal reads all the articles in their entirety. I wonder, however, about the reviewing process and specifically about the reviewers: how were they chosen, and were they all suggested by the authors of the paper? Even more, I wonder whether the authors deliberately withheld the key word intelligent design until the paper was in print and outside the purview of the editors.

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From the abstract:

“This paper describes molecular fine-tuning, how it can be used in biology, and how it challenges conventional Darwinian thinking.”

From the body of the paper [bold type added is mine]:

“A design is a specification or plan for the construction of an object or system, or the result of that specification or plan in the form of a product.”

“Fine-tuning and design are related entities. Fine-tuning is a bottom-up method, while design is more like a top-down approach.”

“William Dembski, who mainly belongs to the frequentist’s school in statistics, regards the fine-tuning argument as suggestive, as pointers to underlying design. … In the case of fine-tuning of our cosmos, design is considered to be a better explanation than a set of multi-universes that lacks any empirical or historical evidence.

Michael Behe and others presented ideas of design in molecular biology, and published evidence of “irreducibly complex biochemical machines” in living cells. In his argument, some parts of the complex systems found in biology are exceedingly important and do affect the overall function of their mechanism. The fine-tuning can be outlined through the vital and interacting parts of living organisms. In “Darwin’s Black Box” … Behe exemplified systems, like the flagellum bacteria use to swim and the blood-clotting cascade, that he called irreducibly complex, configured as a remarkable teamwork of several (often dozen or more) interacting proteins. Is it possible on an incremental model that such a system could evolve for something that does not yet exist? Many biological systems do not appear to have a functional viable predecessor from which they could have evolved stepwise, and the occurrence in one leap by chance is extremely small. To rephrase the first man on the moon: “That’s no small steps of proteins, no giant leap for biology.”

Living forms exhibit structures and functions that can best be understood as nano-level engineering.

“there are presently no detailed Darwinian accounts of the evolution of any such biochemical or cellular system, “only a variety of wishful speculations

Intelligent Design (ID) has gained a lot of interest and attention in recent years, mainly in USA, by creating public attention as well as triggering vivid discussions in the scientific and public world. ID aims to adhere to the same standards of rational investigation as other scientific and philosophical enterprises, and it is subject to the same methods of evaluation and critique. ID has been criticized, both for its underlying logic and for its various formulations …
William Dembski originally proposed what he called an “explanatory filter” for distinguishing between events due to chance, lawful regularity or design.”

It seems silly to me that the editors now object to the keyword Intelligent Design being added. Unless one has been living in a cave the past few decades, the concepts of ID are overt and explicit in the paper. What did they think they were reading?

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Very odd. Did anyone even look at the reference list, which must be chock full of papers from creationist “journals”?

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From Retraction Watch:

According to the journal, Thorvaldsen and Hössjer not only failed to disclose their links to creationists (more on that in a second), but they actively hid their work’s adjacency to intelligent design by leaving that phrase out of their keywords until after the editing process was complete.

As it happens, Thorvaldsen is well-known to creationists, particularly the Discovery Institute, which has included his work in a bibliography of what it considers to be research supportive of its cause.

Meanwhile, Thorvaldsen is the head of an outfit called BioCosmos, which doles out money to people who push intelligent design. Last November, BioCosmos received a $1.6 million grant from Einar Johan Rasmussen, a Norweigian executive partial to the cause, according to this article in Uncommon Descent, a creationist website. The article states that:

Thorvaldsen is also head of the Norwegian branch of Origo, an evolution-critical magazine and publishing company, a collaboration between Danish and Norwegian evolution sceptics and ID proponents.

I’m not sure it makes sense to fault them for “failing to disclose their links to creationism.” Though I might be an issue that they did not disclose in the abstract or title the links to ID.

Elsevier, we note, has stumbled in this arena before. In 2011, they apologized to an author for retracting his creationist-friendly paper — and paid his legal fees after he sued them.

I wonder if this is actually what is driving the strange response from the journal, their past experience with Granville Sewell.

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And now from Coyne and Panda’s Thumb again:

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The co-author Thorvaldsen stated in his reply to Retraction Watch “The paper speaks for itself”. I agree. If the vetting process, editorial and peer review, is deficient, that is a problem with the journal. I do not see that the authors of the paper hid anything; quite the opposite, there is little of ID which is not openly referenced in concept, terminology, and footnotes. The editors own this.

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