Gerdien de Jong was until her retirement Associate Professor in the Department of Biology at Utrecht University

A tale of two papers

In 2021, dr Matthew / Matyas Cserhati published two parallel articles on the affinities of the red panda Ailurus fulgens, one in BMC Genomics and one in Creation Research Society Quarterly. The two articles are mostly based on the same data and have similar and sometimes identical content.

The BMC Genomics article has the title: “A tail of two pandas – whole genome k-mer signature analysis of the red panda (Ailurus fulgens) and the Giant panda (Ailuropoda melanoleuca)”. This paper concludes that on a whole genome level the red panda possibly belongs to the mustelid (marten) clade. The CRSQ article has the title: “Classification of the enigmatic red panda (Ailurus fulgens) based on molecular baraminology-based analysis”. This paper deems it likely that the red panda belongs to the mustelid holobaramin.

The BMC Genomics paper

Cserhati uses two types of data for the phylogenetic placement of the red panda: Whole Genome K-mer Signature (WGKS) and sequence analysis on mtDNA. Cserhati establishes the frequency spectrum of all possible 8-mer base sequences over the whole genome of a species for 28 species. For each species pair a correlation coefficient over 8-mer frequencies can be computed, leading to a correlation matrix of genomic patterning over the species.

Cserhati uses the correlation matrix to find 4 clusters: the eleven cats, the five bears, the skunk, and a cluster containing the martens and the red panda. But then Cserhati writes: “Based on this evidence, (the red panda) would belong to (the marten family) as a monophyletic group.”

Here the article derails.

Continue Reading

This is part 4 of a series of 7 posts by Lars Johan Erkell, with comments on each by Ola Hössjer and a reply by Erkell. Part 1 will be found here. They are translations of 2020 posts in Swedish from the Biolog(g) blog of the Department of Biology of Gothenburg University.

Breakthrough for Intelligent design? (part 4)

November 13, 2020

by Lars Johan Erkell

Non-physical information?

Towards the end of the article, the authors look ahead, towards a future Design Science. We read in the last paragraph:

Biologists need richer conceptual resources than the physical sciences until now have been able to initiate, in terms of complex structures having non-physical information as input (Ratzsch, 2010).

Thorvaldsen and Hössjer refer to a book chapter by philosopher Del Ratzsch, who discusses the epistemological question of whether science can in principle exclude non-material explanations¹. If you now open the book and look at what Del Ratzsch has actually written, you read on page 356:

Biologists need richer conceptual resources than the physical sciences have been able to generate. Historically, design-linked ideas have provided such resources and those resources have been, and continue to be, scientifically fruitful in biology.

This is deplorable. Thorvaldsen and Hössjer have distorted the quote so that it has come to mean something completely different. Del Ratzsch does not mention “non-physical information” in his text at all. Thorvaldsen and Hössjer have invented that.

The cheating is also revealing. Steinar Thorvaldsen is a professor of Information Science, and if “non-physical information” had been a term used in the field, he would of course have referred to the scientific literature. Instead, a quote attributed to a philosopher has been fabricated. It is an acknowledgement that “non-physical information” does not exist as an established scientific concept.

But what in the world could one imagine “non-physical information” to be? The information processing in any case I’ve heard of is always tied to matter of some kind: a brain or a computer. The information is always carried by some material medium, such as visible symbols, sound waves, patterns of magnetization, electromagnetic radiation or something else. The information itself consists, as far as I can understand, of a pattern or structure in the material medium. But how can there be pattern or structure in something that does not exist? Could “non-physical information” somehow float freely in space? Where does it come from? How could it affect matter? How do we even know it exists?

Continue Reading

This is part 3 of a series of 7 posts by Lars Johan Erkell, with comments on each by Ola Hössjer and a reply by Erkell. Part 1 will be found here. They are translations of 2020 posts in Swedish from the Biolog(g) blog of the Department of Biology of Gothenburg University.

Breakthrough for Intelligent design? (part 3)

November 13, 2020

by Lars Johan Erkell (with comment by Ola Hössjer)

Miracles as science?

Thorvaldsen and Hössjer give a number of examples of systems that they think are suitable for the statistical model we discussed in the previous post. One of the examples concerns human evolution.

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; 2016b, Carter et al., 2018, Hössjer and Gauger, 2019).

Since Thorvaldsen and Hössjer raise this question as suitable to study with their statistical model, we shall look at it more closely.

Continue Reading

Photograph by Al Denelsbeck.

Photography contest, Honorable Mention.

This is an additional post by Lars Johan Erkell made on September 8, 2021 in Swedish at the Biolog(g) site after the seven posts of his “Breakthrough for Intelligent Design?” series were made. He has requested that we post it here after the second post in that series, to explain his position in that post on what can be considered legitimate science.

A central point in the discussion I have with Ola Hössjer in the posts entitled "Breakthrough for intelligent design?" concerns the limits for what can be considered legitimate science. Since my responses to his comments on this matter are too long for the comments section, I have made a separate post on the subject.

The central question is how to formulate a hypothesis, that is, a suggested explanation for a phenomenon. Hypotheses are not formulated in an arbitrary way; you don't just grab something out of the air. A hypothesis should be based on prior knowledge. It should also be falsifiable, which means that it must be possible to show that it is incorrect. The scientific work then consists of testing the hypothesis. Whether it proves to be true or false, something new has been learned. The important thing here is that the hypothesis is formulated in such a way that it can be tested in practice with a clear-cut result. If you cannot do that, you cannot learn anything new. And if you cannot test your hypotheses, you cannot root your theories in the real world.

However, just because a hypothesis is falsifiable does not mean that it is scientific. For example, "the Moon is a cheese" is a falsifiable (and falsified) hypothesis. But pure nonsense. If we want to give it a scientific touch, we can formulate it as a classical syllogism:

Premise 1: The Moon is yellow, round and has craters

Premise 2: A cut cheese is yellow, round and has pits that look like craters

Conclusion: The Moon is a cheese

This conclusion is not just grabbed out of thin air; it is based on an analogy. But it is still nonsense. My point here is that just because a hypothesis is falsifiable, or is expressed in a formally correct manner, that does not mean it is plausible or even makes sense.

Continue Reading