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At Mind Matters News: University of Chicago biochemist: All living cells are cognitive

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James Shapiro’s recent paper points out, with examples, that bacteria meet the Oxford English Dictionary’s definition of “cognitive”:

One of the most interesting examples he gives is quorum sensing. At one time, researchers had no idea bacteria were talking to each other about the narrow range of topics that interest bacteria — but talking to each other nonetheless:

News, “University of Chicago biochemist: All living cells are cognitive” at Mind Matters News

The best-known form of interbacterial communication has come to be labelled “quorum sensing” (QS) because it serves to inform a population if it has achieved a critical density for making a regulatory decision (i.e., a quorum). Quorum sensing occurs when the bacteria secrete a chemical “quorum signal” in an autoinduced positive feedback loop but only produce a coordinated multicellular response output when the signal’s concentration exceeds a critical threshold. Quorum sensing is similar to autocrine signalling in complex eukaryotes, and it activates many different processes. The quorum signals come in many chemical forms, and have potential for great specificity, but some signals are also common to multiple types of bacteria, allowing interspecific communication as well.

James A. Shapiro, All living cells are cognitive, Biochemical and Biophysical Research Communications, Volume 564, 2021, Pages 134-149, ISSN 0006-291X, https://doi.org/10.1016/j.bbrc.2020.08.120.

Shapiro is also the author of Evolution: A View from the 21st Century (2013).

It’s awe-inspiring to realize that there is a complex intelligence in every living cell. Two questions arise: Is it the intelligence of the cell? That seems inconsistent with how we usually use the word “intelligence.” If we see that a one-celled life form functions with lot of intelligence, perhaps it is more like a book that contains great ideas. Paper doesn’t create ideas; neither, by itself, does protoplasm. Something else is at work.

Takehome: Future debates over origins of intelligence, consciousness, etc., may mainly feature panpsychists vs. theists rather than materialists vs. theists.

See also: Why do many scientists see cells as intelligent? Bacteria appear to show intelligent behavior. But what about individual cells in our bodies?

You may also wish to read more on the growth of panpsychism as a movement in science:

Scientific American explores panpsychism… respectfully. This is a major change. At one time, a science mag would merely ridicule the idea of a conscious universe. Make no mistake, panpsychism—as Goff elucidates it—is a purely naturalist view (“nothing supernatural or spiritual”). But, unlike the village atheist, he goes on to ask, but then what IS nature? Matter is all there is? But what IS matter? It turns out, no one really knows.

Why would a neuroscientist choose panpsychism over materialism? It seems to have come down to a choice between “nothing is conscious” and “everything is conscious.”

How a materialist philosopher argued his way to panpsychism. Galen Strawson starts with the one fact of which we are most certain — our own consciousness. To Strawson, it makes more sense to say that consciousness is physical — and that electrons are conscious — than that consciousness is an illusion.

Theoretical physicist slams panpsychism Electrons cannot be conscious Sabine Hossenfelder’s view because they cannot change their behavior. Hossenfelder’s impatience is understandable but she underestimates the seriousness of the problem serious thinkers about consciousness confront. There is a reason that some scientists believe that the universe is conscious: It would be more logically coherent to say that you think the universe is conscious than to say that your own consciousness is an illusion. With the first idea, you may be wrong. With the second idea, you are not anything.

Philosopher: Panpsychism is not in conflict with physics at all
Responding to criticism from physicists Sabine Hossenfelder and Sean Carroll, Philip Goff points out that panpsychism is not a dualist perspective. Philip Goff sees panpsychism (consciousness pervades all nature) as offering a simpler view of physics than dualism, with fewer gaps than materialism.

Why is science growing comfortable with panpsychism (“everything is conscious”)? At one time, the idea that “everything is conscious” was the stuff of jokes. Not any more, it seems. A recent article at New Scientist treats panpsychism as a serious idea in science. That’s thanks to the growing popularity of neuroscientist Giulio Tonioni’s Integrated Information Theory (IIT), which offers the opportunity for mathematical modeling, along with the implication that inanimate matter and/or the universe may be conscious. If IIT continues to gain a sympathetic hearing, panpsychism could become, over time, a part of normal science.

In my view James Shapiro, (and Perry Marshall), are confusing simple 'cognition' with creative 'intelligence'.
cognition - "connected with mental processes of understanding" - Oxford Dictionary "Cognition—sensing and responding to the environment",,, - Perry Marshall
It is hard to argue against James Shapiro's, (and Perry Marshall's), contention that bacterial cells must have some sort of cognitive capacity within themselves that allows them to be aware of their environment and to communicate, and respond, is such a sophisticated fashions as they do.
Learning from Bacteria about Social Networking (Information Processing) - video Excerpt: I (Dr. Ben-Jacob) will show illuminating movies of swarming intelligence of live bacteria in which they solve optimization problems for collective decision making that are beyond what we, human beings, can solve with our most powerful computers. http://www.youtube.com/watch?v=yJpi8SnFXHs
But, in my honest opinion, where James Shapiro, (and Perry Marshall), go off the rails is that they, without empirical evidence, have presupposed that this 'rudimentary' cognitive capacity within bacterial cells is sufficient, within itself, to explain the creation of new biological information over and above what is already present in life. It isn't, for that you need 'intelligence', not merely 'cognition' as Shapiro, and Marshall, have erroneously presupposed. As Stephen Meyer explained in chapters 15 and 16 of his book 'Darwin's Doubt', (where he addressed Shapiro's 'cognitive' model, along with addressing several other 'post-neo-Darwinian models'), "although several of these new evolutionary theories offer some intriguing advantages over the orthodox neo-Darwinian model, they too fail to offer adequate explanations for the origin of the genetic and epigenetic information necessary to account for new forms of animal life."
Lynn Margulis: Evolutionist and Critic of Neo-Darwinism - Stephen C. Meyer - April 25, 2014 Excerpt: in Chapters 15 and 16 of Darwin's Doubt, I addressed six new (that is, post neo-Darwinian) theories of evolution -- theories that proposed new mechanisms to either supplement or replace the reliance upon mutation and natural selection in neo-Darwinian theory.,, I show that, although several of these new evolutionary theories offer some intriguing advantages over the orthodox neo-Darwinian model, they too fail to offer adequate explanations for the origin of the genetic and epigenetic information necessary to account for new forms of animal life -- such as those that arise in the Cambrian period. http://www.evolutionnews.org/2014/04/lynn_margulis_e084871.html AUDIOBOOK & PDF - Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design by Stephen C. Meyer https://archive.org/details/ddbscm
Neo-Darwinism, nor Shapiro's 'cognitive' model of 'Natural Genetic Engineering', (nor any of the other 'post Neo-Darwinian' models that have been offered), have any empirical evidence whatsoever that their models can create new genetic and epigenetic information over and above what is already present in life. For instance, in regards to proteins, Tawfik and Tóth-Petróczy wrote, “In fact, to our knowledge, no macromutations ... that gave birth to novel proteins have yet been identified.”
Dan S. Tawfik Group - The New View of Proteins - Tyler Hampton - 2016 Excerpt: Tawfik soberly recognizes the problem. The appearance of early protein families, he has remarked, is “something like close to a miracle.”45,,,,,, “In fact, to our knowledge,” Tawfik and Tóth-Petróczy write, “no macromutations ... that gave birth to novel proteins have yet been identified.”69 http://inference-review.com/article/the-new-view-of-proteins
There is simply no empirical evidence in the peer-reviewed literature at large, nor in Shapiro's, (or Marshall's), present paper, that life, all by its lonesome, (and no matter how sophisticated the 'cognitive' responses of cells may be), can create information over and above what is already present in life. In fact, a recurring theme that comes from the scientific evidence itself turns out to be that the vast majority of 'beneficial' adaptations, no matter how sophisticated those 'cognitive' adaptations may be, are the result of a loss of genetic information, not the result of a gain of genetic information,
“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.? - per uncommon descent Getting There First: An Evolutionary Rate Advantage for Adaptive Loss-of-Function Mutations Michael J. Behe - 2013 http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0020 Michael Behe: Darwin Devolves – 2019 video - Eric Metaxas, (at Socrates in the City), interviews biochemist Michael Behe on "the new science about DNA that challenges evolution" as told in Behe's book, ‘Darwin Devolves’. https://www.youtube.com/watch?v=QNe-syuDJBg Also see, John Sanford's book "Genetic Entropy": Genetic Entropy - John Sanford – November 7, 2014 - Genetic Entropy presents compelling scientific evidence that the genomes of all living creatures are slowly degenerating - due to the accumulation of slightly harmful mutations. This is happening in spite of natural selection. - per amazon
Whereas, although we have no evidence whatsoever that 'cognition', all by its lonesome, (and no matter how sophisticated that cognition of cells may appear to be), can create new genetic information over and above what is already present in life, on the other hand we do, at least, have evidence that human intelligence can and does habitually and routinely create new information that has not existed before. Shoot, Shapiro's, and Marshall's, papers, in and of themselves, demonstrate the creation of new information that did not exist in the universe before. Shoot, even Perry Marshall, (in his present 'cognition' paper, and although he offered no examples of 'cell cognition', all by its lonesome, creating new genetic information, and/or 'codes'), himself recognized the 'creation of new information problem'.
Biology transcends the limits of computation – Perry Marshall – Oct. 2021 Excerpt: 4.4. There is a severe limit on the size of useful statements that can be generated by randomness The statistical syllogism in support of the above statement is as follows: 1. For a computer to generate specific statements consisting of more than 332 bits of information (42 bytes, or 42 letters) through a random “brute force” process requires 10^100 trials to test all combinations 2. 10^100 trials could not be made by any real-world computer in the history of the universe. 3. Therefore, specific statements longer than 332 bits are not realizable through randomness. https://www.sciencedirect.com/science/article/pii/S0079610721000365?via%3Dihub
Although I very much liked Perry Marshall's 'cognition' paper, and thought that he made several important points in his paper, it seems that Marshall missed some rather glaring and obvious points in his paper. For instance, Marshall lists the falsification criteria of his 'cognition' hypothesis as such,
5.3. Falsification Any experiment that demonstrates chemicals can give rise to code without inserting biological cognition will show the model proposed in this paper to be wrong (“Origin Of Life: $10 Million Prize at the Royal Society,” 2019),
Yet, in the abstract Marshall specifically states that,
"According to the reductionist view, the causal chain in biology is chemicals ? code ? cognition.,,, the correct causation sequence is cognition ? code ? chemicals."
Thus, since, according to Marshall's own abstract, cognition must precede the existence of 'code', and 'code' precedes the existence of biological life, then clearly Marshall is holding that 'cognition' must precede biological life, yet Marshall is also presupposing in his falsification criteria, (and without any listed evidence that 'biological cognition' can create codes I might add), and contrary to what he had directly stated in his abstract, that 'biological cognition' can create codes. Specifically he stated in his falsification criteria that, "Any experiment that demonstrates chemicals can give rise to code without inserting biological cognition will show the model proposed in this paper to be wrong". I'll go Perry Marshall one better in my falsification criteria for Intelligent Design, "Any experiment that demonstrates that 'biological cognition', all by its lonesome, can give rise to 'code', without inserting "creative intelligence' into the experiment somewhere, will show the Intelligent Design model to be wrong".
1 Thessalonians 5:21 but test all things. Hold fast to what is good.
As I stated yesterday in Marshall's "Biology Transcends The Limits Of Computation" thread, "Christians have been postulating that life has an author for 2000 years now. Long, long, before DNA and “negentropy” was even known about." https://uncommondesc.wpengine.com/biology/researcher-biology-transcends-the-limits-of-computation/#comment-739635
Acts 3:15 You killed the author of life, but God raised him from the dead. We are witnesses of this. John 1:1-4 In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. In him was life, and that life was the light of all mankind.

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