How to “cook science”

50% of peer reviewed articles may be not true…How’s that possible? You pay $ and the articles with the results you would like them to be get cooked for you in the most prestigious science journals in the world.

In the video there is also an interesting bit on the cholesterol lowering statins issue in France…Big Pharma demands to put statins in the water…or people will die…

Of “models” and “algorithms”

I was short with Joe Felsenstein in the comments section of “Stark Incompetence,” a post in which I address, well, um, the stark incompetence on display in a recent publication of Eric Holloway. I have apologized to Joe, and promised to make amends with a brief post on the topic that he wants to address. Now, the topic is a putative model that Eric introduced in “Mutual Algorithmic Information, Information Non-growth, and Allele Frequency” (or perhaps an improved version of the model). Here is a remark that I addressed to Joe:

Tom English: As you know, if a putative model is logically inconsistent, then it is not a model of anything. I claim that that EricMH’s putative model is logically inconsistent. You had better prove that it is consistent, or turn it into something that you can prove is consistent, before going on to discuss its biological relevance.

I will not have to go far into Eric’s post to identify inconsistencies. After explaining the inconsistencies, which I doubt can be eliminated, I will remark on why the “model” is not worth salvaging. The gist is that Eric’s attempted analysis puts a halting, output-generating simulator of a non-halting, non-output-generating evolutionary process in place of the process itself. An analysis of the simulator would not, in any case, be an analysis of the simuland.

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Stark incompetence

David Nemati and Eric Holloway, “Expected Algorithmic Specified Complexity.” Bio-Complexity 2019 (2):1-10. doi:10.5048/BIO-C.2019.2. Editor: William Basener. Editor-in-Chief: Robert J. Marks II.

Let us start by examining a part of the article that everyone can see is horrendous. When I supply proofs, in a future post, that other parts of the article are wrong, few of you will follow the details. But even the mathematically uninclined should understand, after reading what follows, that

  1. the authors of a grotesque mangling of lower-level mathematics are unlikely to get higher-level mathematics correct, and
  2. the reviewers and editors who approved the mangling are unlikely to have given the rest of the article adequate scrutiny.

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Shifting paradigms

Are we beginning to see a major paradigm shift, steadily moving away from the prevailing physicalist, materialist.mechanistic mindset?

Integral theory is one attempt to move beyond any narrow,exclusive views of reality proclaimed by representives of science, religion, philosophy, spiritual traditions or whatever. Jennifer Gidley writes about integral thinking and the evolution of consciousness here

There are periods in human and cultural evolution when humanity passes through such fundamental transformations that our reality shifts and new patterns of thought are required to make sense of the unfolding human drama . . . The profound transformation we are now witnessing has been emerging on a global scale over millennia and has matured to a tipping point and rate of acceleration that has radically altered and will continue to alter our human condition in every aspect. We must therefore expand our perspective and call forth unprecedented narrative powers to name, diagnose, and articulate this shift… Integral philosopher Ashok Gangadean in the opening quotation encapsulates what many integral theorists have been voicing over the past decade. It is this integral research on emergent movement(s) of consciousness that I am referring to as the evolution of consciousness discourse This research points to the emergence of a new structure,stage(s) or movement of consciousness that has been referred to by various terms, most notably, post-formal integral and planetary.

Jude Currivan says that instead of big bang we have the big breath. The “outbreath” that gives rise to the physical unverse. Matter and energy are the products of information. The physical universe is in-formed as she puts it.


She discusses her views here in “Restating and reunifying reality: Our in-formed and holographic universe”.


This is part of an annual Mystics and Scientists conference promoted by The Scientific & Medical Network


The metaphor of the big bang conjures up images of a destructive explosion leading to chaos. But we should imagine the universe as a birth of order and organisation and this is more in keeping with a breathing process by which we communicate compositions of song, poetry and prose. Evolution is the creation of order out of chaos.


So are we seeing a movement to a more integrated, holistic understanding of reality where, rather than being a mere by product of a particular arrangement of matter, consciousness plays a primal, central role? The cosmos is breathed into existence, the out-breathing Word, the Logos, creates the living universe. Consciousness is the alpha and omega.

Non-conservation of algorithmic specified complexity…

… proved without reference to infinity and the empty string.

Some readers have objected to my simple proof that computable transformation f(x) of a binary string x can result in an infinite increase of algorithmic specified complexity (ASC). Here I give a less-simple proof that there is no upper bound on the difference in ASC of f(x) and x. To put it more correctly, I show that the difference can be any positive real number.

Updated 12/8/2019: The assumptions of my theorem were unnecessarily restrictive. I have relaxed the assumptions, without changing the proof.
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A Conflation of Atheisms

In all the discussions of atheism, I have not yet seen any one make what I take to be a rather simple point: atheism is always relative to a specific conception of God. For this reason, one can be an atheist in one sense and a theist in another. This in turn raises the question whether an atheist is intellectually compelled to investigate every conception of God and refute each of them in order to be entitled to his or her atheism. I want to make a preliminary, crude, and rather obvious distinction between two ways of conceiving of God in order to clarify two distinct kinds of atheism: the mythological conception and the metaphysical conception.

On how the fear/dread of man upon creatures, given by God after the flood, also manifests itself in creatures fear of each other by bright coloration of their bodies.

After the flood God said the fear/dread of man would be upon all creatures on earth. birds, insects, animals , fishes. this was needed because, seemingly , for the first time man would be intimate with biology and so in danger. thus man had this innate protection. YET how does this work? Is it in the thoughts of creatures?

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Breaking Down Barriers

In the video Moral Technology Conference 2016: Day 1 Lecture 1, NIcanor Perlas advocates participating in global conversations which break down the barriers of compartmentalization.

I share his belief that whoever has the money and power, their vision will be the de facto world we are living in, Those with the power make the prominent worldview, the only worldview that is allowed to be taken seriously. Whether or not it is in keeping with reality it will eventually become reality.

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Evo-Info 4 addendum

Introduction to Evolutionary Informatics, by Robert J. Marks II, the “Charles Darwin of Intelligent Design”; William A. Dembski, the “Isaac Newton of Information Theory”; and Winston Ewert, the “Charles Ingram of Active Information.” World Scientific, 332 pages.
Classification: Engineering mathematics. Engineering analysis. (TA347)
Subjects: Evolutionary computation. Information technology–Mathematics.

In “Evo-Info 4: Non-Conservation of Algorithmic Specified Complexity,” I neglected to explain that algorithmic mutual information is essentially a special case of algorithmic specified complexity. This leads immediately to two important points:

  1. Marks et al. claim that algorithmic specified complexity is a measure of meaning. If this is so, then algorithmic mutual information is also a measure of meaning. Yet no one working in the field of information theory has ever regarded it as such. Thus Marks et al. bear the burden of explaining how they have gotten the interpretation of algorithmic mutual information right, and how everyone else has gotten it wrong.
  2. It should not come as a shock that the “law of information conservation (nongrowth)” for algorithmic mutual information, a special case of algorithmic specified complexity, does not hold for algorithmic specified complexity in general.

My formal demonstration of unbounded growth of algorithmic specified complexity (ASC) in data processing also serves to counter the notion that ASC is a measure of meaning. I did not explain this in Evo-Info 4, and will do so here, suppressing as much mathematical detail as I can. You need to know that a binary string is a finite sequence of 0s and 1s, and that the empty (length-zero) string is denoted \lambda. The particular data processing that I considered was erasure: on input of any binary string x, the output \mathtt{erased}(x) is the empty string. I chose erasure because it rather obviously does not make data more meaningful. However, part of the definition of ASC is an assignment of probabilities to all binary strings. The ASC of a binary string is infinite if and only if its probability is zero. If the empty string is assigned probability zero, and all other binary strings are assigned probabilities greater than zero, then the erasure of a nonempty binary string results in an infinite increase in ASC. In simplified notation, the growth in ASC is

    \[A(\mathtt{erased}(x)) - A(x) = \underbrace{A(\lambda)}_\text{infinite} - \underbrace{A(x)}_\text{finite} = \infty\]

for all nonempty binary strings x. Thus Marks et al. are telling us that erasure of data can produce an infinite increase in meaning.

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Number of Unique Commentators

For The Panda’s Thumb’s After the Bar Closes thread on Uncommon Descent, I created a graph of the number of unique commentators at UD:

Here, for each day from Apr 2005 until Nov 2019, I gave the number of different people who commented at UD at least once during the previous 365 days. The colors indicate the number of contributions such a commentator has made over this period of time.

Obviously, the same can be done for “The Skeptical Zone”:

Enjoy!

The REAL “Problem of Evil”

[moderator’s note: Nonlin.org produced this at about the same time as his “Miracles” post. I delayed this, so that they could be discussed one at a time. I’m now publishing this one.]

[a note to nonlin – if all of your post is one block, it is hard to add a “more” break. Maybe a short introductory sentence as a first block would make that easier]

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Behe and Co. in Canada

This past Friday, I bumped into Dr. Michael Behe, and again on Saturday, along with Drs. Brian Miller (DI), Research Coordinator CSC, and Robert Larmer (UNB), currently President of the Canadian Society of (Evangelical) Christian Philosophers. Venue: local apologetics conference (https://www.diganddelve.ca/). The topic of the event “Science vs. Atheism: Is Modern Science Making Atheism Improbable?” makes it relevant here at TSZ, where there are more atheists & agnostics among ‘skeptics’ than average.

On the positive side, I would encourage folks who visit this site to go to such events for learning/teaching purposes. Whether for the ID speakers or not; good conversations are available among people honestly wrestling with and questioning the relationship between science, philosophy and theology/worldview, including on issues related to evolution, creation, and intelligence in the universe or on Earth. Don’t go to such events expecting miracles for your personal worldview in conversation with others, credibility in scientific publications or in the classroom, if you are using ‘science’ as a worldview weapon against ‘religion’ or ‘theology’. That argument just won’t fly anymore and the Discovery Institute, to their credit, has played a role, of whatever size may still be difficult to tell, in making this shift happen.

A question arises: what would be the first question you would ask or thing you would say to Michael Behe if you bumped into him on the street?

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The New Atheism: A Failed Hamartiology

It is sometimes useful to remember that The Skeptical Zone was started in the naive assumption that intelligent people of good will could discuss important issues without undue rancor. (Ha ha ha!! Have you even seen the Internet!)

Anyway, I bring to your attention a rather interesting blog post (blogs? who blogs anymore?) by Scott Alexander over at Slate Star Codex: ” New Atheism: The Godlessness That Failed“. Alexander gives us some interesting data (frequency of search terms taken from Google and other sites) that document a flagging interest in the “religion vs atheism” debates of the early 2000s.

Here are two (I think) revealing quotes that contextualize the decline of New Atheism in terms of changes in Internet culture:

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Metaphors

These days researchers are obsessed with making models as an aid to understanding reality. But there is a danger here in that in concentrating on the models the actual living world around us is lost sight of. And the same can be said regarding the metaphors that are in frequent use. How true to reality is the mind picture evoked by the metaphor.

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Did Richard Feynman say methodological naturalism would fail in matters of science?

YES! If I understand him correctly!

Methodological Naturalism(MN) on TSZ and everywhere comes up in origin matters all the time. Are present mechanisms/machinery for the universe always been acting as is and so negates the involvement of a creator who would need to interfere and did?

all biology and geology and cosmology researchers want common laws to be fixed in the universe and any creationism is frustrated right out of the gate. for fun and profit i recently watched the Richard Feynman lectures on physics. He is still remembered by older people as a important scientist . i’m not sure his accomplishments back this up and instead its a old prejudice about post war physics mattering greatly. possibly he just tied up some loose ends. however his true science status is not the point. The point is that the science “community’ know his name and care what he thinks about science generally. On youtube on the fifth lecture Character of physical law(The distinction of past and future) starting at 16:40-22:10 minutes on it HE brings up about geology, history, cosmology as being different then physics. He complains this is a error. physics must of evolved TOO. The present laws of physics must of been different then the past ones while it was evolving. The present is not a accurate portrayal of the past based on this idea. THE universe/world was MORE organized in the past. Outside the province of present physic laws. On another youtube show called “Take the world from another point of view” by same author. on the third video at 9:00 he says the same thing. in short m==MN does not work with present systems because they radically must of evolved from a more organized past system. SO boundaries based on present laws of nature would fail to accurately explain things. this is important idea for creationism in so much.In biology or geology or cosmology its reasonable to imagine , as options, that present laws, whether on creation week, post fall, post flood, could easily be different then present laws in these subjects. unless someone says Mr Feynman is wrong!!

Rejected for ideology only

A TSZ member recently made this claim:

Sanford’s recent paper with Cordova was rejected by multiple venues for bogus reasons. Everyone agreed the science is solid, but made up reasons why the paper should not be accepted.

And then is asked:

Name the venues and give their reasons for the rejection. 

I’ve actually been asking this for literally years over at UD, although not lately. The claim that papers are rejected not because of the science but instead because of some other reason is often made. But I’ve never seen any actual evidence of this. Has anyone?

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On Ideology. Between Secular & Secularism – what’s the similarity, difference or overlap?

Adding to that a 2nd question: If a person seeks ‘secularization’ (cf. laïcisation), i.e. ‘more secularity’ in their life and in the lives of those around them, in their hometown and in the nation in which they live, and even globally, does that qualify for the operational term ‘secularist’? In this sense, is ‘secularism’ the proper term for the ideology that such a person is promoting?

One might think it a polite necessity for certain voices to avoid all contact, and any proper and timely discussion of ideology, when addressing these two terms – secular & secularism – semantically, philosophically & especially ‘skeptically’. Some people of course just don’t make a priority focus on ideology, as Paul Nelson recently revealed here (re: ideological MNism, while avoiding ideological IDism), saying “‘Ideology’ is fine with me as a descriptive noun,” but is “[n]ot one of my lexical habits”. Even though Nelson is certainly not representative of TSZ voices, it might make a person wonder if there is a healthy skepticism at TSZ about conflating the terms ‘secular’ & ‘secularism’, since it has also proven difficult here to differentiate them, just as it has at Peaceful Science. For others, the notion that ‘secular’ is now broadly considered as a condition, while ‘secularism’ counts as an ideology, isn’t all that difficult to acknowledge and accept.

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Categorization and measurement

In a recent comment, BruceS suggested that I do an OP on categorization and measurement, so here it is. I’ll try to keep this short, but later extend it with posts in the thread. If my post in the thread begins with a bold title, then it is intended to extend the OP. And I may then add a link, if I can figure out this blocks editor.

I’ll start with a link to a paper by Stevan Harnad (this blocks editor is annoying).

Cognition is categorization

Harnad’s paper is not quite how I am looking at it, but it gives a good introduction to the idea.

Red, blue or green? That’s a question about categorizing by color. We also categorize by size. Measurement is just a mathematical way of categorizing by length or by voltage or by pressure — by whatever we are measuring.

We categorize as a way of getting information. Within science, information is often acquired by measuring, which is a type of categorizing. I can get information with a digital camera. The digital camera, in effect, categorizes the world into pixel sized chunks and provides data for each of those.

What is categorization?

Categorization just means dividing up into parts. We divide up in accordance with features. Harnad discusses this in an appendix near the end of the linked paper.

There’s an alternative view of categorization, suggested by Eleanor Rosch, where categorization amounts to grouping things in accordance with their similarity to some sort of prototype or family resemblance. Harnad looks at that in the appendix, and he does not agree with Rosch. I concur with Harnad on that.

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