This is the third and last of a series of posts on the misguided concept of “agency and purpose in biology,” which one can take as the statement that “organisms have goals, and guide their own development and evolution towards those goals”.
In my first post, on December 23, I noted that the John Templeton Foundation (JTF) was spending millions of dollars funding grants on the science of “purpose and agency”. I pointed out one JTF grant that just ended, which handed out $14.5 million to a consortium of investigators to study this topic. And the JTF intends to continue funding this area:
Science of purpose. We are looking for experimental and theoretical research projects that will provide insight into the purposive, goal-directed, or agential behaviors that characterize organisms and various components of living systems. Researchers who have familiarity with our ongoing work in this area are especially encouraged to apply.
If you know the JTF, you’ll understand why they keep replenishing a trough full of grant money for such studies, for John Templeton (a mutual-fund billionaire and a believer) funded his Foundation with the intent of showing that science itself gave evidence for “spiritual reality”, aka a god or gods. Although some of the investigators supping at the trough deny that they’re engaged in teleology, much less giving evidence for divinity, all of their work feeds into the JTF’s mission, and the authors of an article just published online at the Journal of Evolutionary Biology (JEB) agree: the idea of teleology sneaks into many of these papers.
In my second post, on December 26, I analyzed one of the JTF-funded papers often cited to support the idea of agency and purpose in organisms, a paper in BioEssays by Sonia E. Sultan et al. I found it vacuous and intellectually confusing, mistaking “purpose” and “agency” for the results of natural selection and, in the end, making the ID-friendly argument that neo-Darwinism cannot explain the origins of “novel, complex traits”. That assertion alone discredits the paper, for the one paper that actually tried, using conservative assumptions, to mathematically model the origin of a complex trait (the camera eye), did so very successfully. No problems encountered! The purpose-and-agency folks’ view is that “since we don’t fully understand how an eye/wing/brain evolved, there must have been something beyond natural selection involved.” I suspect you know the fallacy of this argument.
Here are two concepts of agency advanced by Sultan et al and quoted in the paper below:
● “Biological agency—the capacity of living systems […] to participate in their own development, maintenance, and function” (Sultan et al 2022, p. 1);
● “Organisms themselves actively shape their own structure and function” (Sultan et al 2022, p. 4);
Now, a paper by James DiFrisco and Richard Gawne, published in JEB, takes apart the whole misguided notion and program of “agency and purpose” in evolution, and cites a lot of papers that tried to advance misguided ideas similar to those of Sultan et al. The title of the new paper is below, but if you click on it you will go to a truncated version of the article. However, you can read the entire paper as a pdf file available for free here.
Here are what I take as the paper’s important points:
A.) The idea that organisms direct their own development and evolution through some nebulous, non-neo-Darwinian process is incorrect. Everything touted as “purposeful” and “the results of agency” can be explained by natural selection molding organisms’ responses to a changing environment, both within one lifetime or across generations. As DiFrisco and Gawne say, goal-directedness “is an adaptation due to natural selection.” In my own example, cats and other mammals often grow longer fur during cold seasons because natural selection has favored genes that give organisms the capacity to put out more fur when their bodies detect cold weather. This is simple natural selection, and there is no “purpose” or “agency” involved.
B.) Some of the papers on purpose and agency aim to “rescucitate the Aristotelian view of biological purpose and teleology as real rather than merely apparent”, so some authors really do have a teleological bent, one that you can find in some works of the “Extended Evolutionary Synthesis.”
C.) The agency and purpose trope is, in the end, a metaphor that does no explanatory work nor promotes further research. Only the framework of neo-Darwinism can help us understand the origin of adaptations.
D.) The only “true” purpose and agency we see in biology is that which we see in the cognition of organisms capable of responding to environmental challenges by thinking rather than by a mechanical response. But even the p&a authors are the first to aver that this is not the sense in which they use these terms. In truth, as a hard determinist I see even cognition as a mechanical process and not something different in principle from a bacterium moving towards food, but this is not so important in this debate since the “cognition” view of purpose isn’t the subject of scientific work by the Templeton-funded authors.
I’ll quote the authors’ own conception of their aims as given in the JEB paper:
Box 1: The central claims of this paper.
1. An organism’s capacity for goal-directed behavior does not itself explain any biological phenomena. Apparently goal-directed behaviors are, instead, something to be explained as an evolved characteristic of biological systems.
2. The capacity for goal-directed behavior (outside of human cognition, which can set arbitrary, novel goals) is explained by Darwinian natural selection acting in populations of individuals.
3. Notions such as self-determination, or the idea that the whole organism is a cause of its own developmental or physiological processes, are either empirically untestable, or restatements of ordinary questions about which causal mechanisms at which scales influence events.
4. Downward causation and context-dependence are “mechanistic” in the sense relevant to experimental biology. They are not mysterious processes that require adopting the teleological form of investigation provided by an agency perspective.
5. Rejection of molecular reductionism or determinism does not necessitate a commitment to the idea of biological agency. Researchers need not embrace the agency perspective in order to acknowledge the importance of multi-level complexity, emergence, and downward causation.
6. The idea that biological goal-directedness is a product of natural selection rather than the inherent agency of organisms does not require commitment to the idea that all traits are adaptations. It is compatible with genetic drift, mutation, and developmental constraints playing an important role in evolution.
7. Agency is a psychological concept with origins in heuristic ascriptions of intentionality. Accordingly, it is applicable only where psychological explanations are useful—i.e., when explaining the behavior of humans and possibly other neurologically complex organisms such as primates.
8. Agency is not an empirically meaningful property, and incorporating the agency concept into experimental practices will not contribute to progress in biology.
And a few quotes that underline their contentions (indented). First, the important of natural selection in explaining adaptations:
It is important to recognize that the attribution of non-fitness-related goals to an organism can only be empirically grounded in the psychological case, where investigators can ask another human being to report on their internal cognitive states. For systems that lack the capacity to report on such states, the attribution of goals is empirically unmoored and arbitrary (see Fig 1). Is it the goal of a given stem cell to differentiate? (Manicka and Levin 2019; Levin 2021; 2022) Or, if the stem cell fails to differentiate and dies, was that really its goal? In order for goal-attributions to explain anything, goals would need to be linked to some empirically detectable feature of the system other than the actual outcomes of its behavior. Otherwise, these explanations would be circular and uninformative. It is not clear that this can be done without reference to natural selection.
The intellectual and biological vacuity of adding “purpose” to already-existing explanations:
Even if one allows explanations based on agency, it is difficult to see how such explanations could be useful for understanding an ordinary biological process—e.g., wound healing. To explain why a wound heals following injury, the statement that it is because the system possesses agency and pursues the goal of healing wounds is not useful from a scientific point of view. This is because agency is not an experimentally meaningful property that can be subjected to tests as to whether its presence or absence influences wound-healing. The “goal” of wound-healing is not something that can be detected or measured, but would have to be inferred and attributed ex post facto based on the system’s actual behavior (see above, “Agency and goal-directedness”). This procedure cannot predict that wound-healing fails in pathological cases (e.g., tumorigenesis), nor can it explain why such malfunctions do or do not happen. In the context of modern biological research, wound-healing is understood to be explainable in terms of complex positive and negative feedback mechanisms in which a wide array of signaling molecules mediate the progression through cell- and tissue-level processes, from wound detection to hemostasis, inflammation, cell proliferation, re-epithelialization, and tissue remodeling (Singh et al 2017; Rodrigues et al 2019). These feedback mechanisms are tuned to parameter values conducive to survival and reproduction because of natural selection.
Between mechanistic explanations and adaptive ones (Tinbergen 1963; Stearns 1982), there is no obvious role for a distinct form of explanation based on agency.
How could you investigate how wounds heal by even considering the idea of “purpose and agency”? As the authors note, there is no real “goal” here, but merely the sorting-out of genes that have different effects on wounds, with the genes that contribute to healing leaving more copies (their bearers survive and/or reproduce better). That’s simply natural selection. Ergo, there is no scientific benefit of JTF giving lots of dollars to study agency and purpose. They could give money for studying neo-Darwinian explanations, which we know are often the way to go, but doing so would simply justify scientific materialism, something anathema to JTF, as it leaves out god.
Finally, one more quote, as you can read the paper yourself (it’s written very clearly and should be accessible to those with a smidgen of biology knowledge):
An initial difficulty with the notion of self-determination centers on the self. It is not clear how to interpret expressions such as “the capacity of living systems […] to participate in their own development.” Development is the process of an organism going through the stages of its life cycle. It is not something separate from the organism. So how can an organism fail to participate in its development? If we suppose that the development of a given organism is fully determined by a set of underlying molecular factors, it is still the development of that particular organism rather than of another entity. It is also difficult to interpret the statement that “typical descriptions […] treat organisms [as] separate from and passive to the conditions under which they develop and evolve” (Nadolski and Moczek 2023, p. 3). If this refers to environmental conditions, it is an ordinary question of the relative causal importance of internal versus external factors. If it refers to internal conditions, however, the statement veers into obscurity. How can an organism be or separate from, or passive to, a process of development of itself?
This quote—and indeed, the whole paper—shows that the “purpose-and-agency” school is either engaged in a semantic rather than a biological argument, they are simply unable to grasp evolution, or they wish to make a name by couching neo-Darwinian mechanisms in “I-have-a-new-paradigm” language. . Indeed, epigenetics (at least some forms) were not part of the modern synthesis, but neither do they play into notions of agency and purpose. Epigenetic modifications can be evolved features of organisms that are ultimately coded in the genome, or they can be environmentally-induced modifications of DNA that are rarely adaptive and, at any rate, usually disappear in two or three generations at most, making them useless to explain the evolution of adaptations.
The lesson is twofold. Beware when you see biologists banging on about agency and purpose, and think about natural selection instead. Second, the JTF is throwing away its money on misguided projects. I’d like to ask them to give money to fund real biology, as they have over a billion dollars in endowment, but funding real biology would not advance the JTF’s purpose of finding the numinous using science.
This quote caught my eye – is this sort of scare quotes to paraphrase an idea, or is it from the article?:
“organisms have goals, and guide their own development and evolution towards those goals”
The article link timed out.
My comment was to be :
See these two authors/publications for background for the idea of, broadly/crudely, controlling evolution – of human race and more – e.g. the planet, the cosmos :
New Genesis – Shaping a Global Spirituality
Robert Muller
(the U.N. one, not the U.S. FBI one)
1982
The Phenomenon of Man
(Essay)
Pierre Teilhard de Chardin (Jesuit/Catholic priest)
1955 (posthumous)
And perhaps, of course, Deepak, though he’s more into cosmic consciousness.
Thanks, Bryan
Whenever I see a reference to The Phenomenon of Man , I think it’s always worth quoting this bit from Peter Medawar’s review;
Yes! So “good”!
I believe reader Steve Pollard also directed me to Medawar’s essay.
I did indeed, Bryan; and here is the whole thing again! I strongly commend it to anyone who values science above woo: http://bactra.org/Medawar/phenomenon-of-man.html
Richard Dawkins’ response to a bizarre attack on “The Selfish Gene” by philosopher Mary Midgley is as an entertaining read as Medawar’s summation of de Chardin’s book.
And so on ..
https://joelvelasco.net/teaching/3334/dawkins_defense_selfish_genes.pdf
Agency” and “purpose” are totally made-up concepts. They do not exist in nature. However, the words themselves must refer to something. It is too easy for people to learn to use them “correctly” (and to pick out “incorrect” usage) for them not to refer to something in particular.
It would be helpful if someone could define, with dictionary-like conciseness, what people are actually referring to when they use the words agency and purpose. Until such definitions are provided, I fear that the very existence of these words will continue to mislead and deceive
” “Agency” and “purpose” are totally made-up concepts. They do not exist in nature. ”
+1000
Some would say “BASED” – I do.
BASED
Que? We “exist in nature”. We exhibit purpose / agency / intentionality, whatever you take these to mean. Ergo purpose / agency / etc. do manifestly exist in nature, via us, unless your notion of nature directly excludes such things. Or have I fallen down some semantic rabbit hole here?
As a side issue, LOTS of fictional things which surely do not “exist in nature” can be described well enough for people to learn to think about them correctly. Santa Claus is a topical example.
Well yes, in a sense everything exists in nature. But most of us find it useful to make a distinction between fact and fiction, and totally made-up concepts like agency and purpose are fiction–not real things like electrons and exoplanets.
And of course you’re correct that there are “LOTS of fictional things which surely do not ‘exist in nature'” but can be described well enough to serve as semantic content. Agency and purpose are among them.
Teleonomy and agency as concepts have been championed for decades by a small, but ardent group of advocates. To mostly little avail. We (myself and several graduate students) recently read through the edited volume on the topic by Corning et al as a course project. We noted two things: the many authors are almost all male and 60++ years old. It seemed like the book was a last, best attempt to sell the concepts to the next generation of evolutionary biologists (i.e., the grad students). If that was the ‘goal’, it utterly failed across all the students. You can read our short review of the book in the Quarterly Review of Biology (Speck et al. https://www.journals.uchicago.edu/doi/full/10.1086/730655). In short, the future of teleonomy in the next generation looks bleak.
Thanks for the link.
Life is based on the genetic code, which is a system of symbolic representation.
A system of symbolic representation is abritrary and thus cannot be the result of deterministic or random mechanical forces but requires intentionality/teleology in order to assign arbitrary syntactic rules and semantic relations.
Therefore, the genetic code, with its syntax (non-coding regulatory sequences, protein-coding genes, exon/intron boundaries, start/stop codons) and semantic relations (specific codons representing specific amino acids) implies irreducible teleology at the heart of biological phenomonena. In biology, there is intentionality/teleology/purpose all the way down.
I don’t think this is correct. In fact, I think it is nonsense. The genetic code is biochemistry, it is constrained by atomic forces and shaped by natural selection. It is no more teleological than any other kind of chemistry.
Do you know of any chemical reactions, outside of living cells, that are based on a code ? Chemistry dosen’t produce codes. Chemicals don’t represent other chemicals. But codons do represent amino acids. You can “program” a cell to produce any protein you want. You can write down the protein in nucleotide language on a piece of paper first before you implement it in life…
Sorry, but there is plenty of evidence that a code can evolve by natural selection. To say that it’s evidence for some kind of teleological force is nonsense.
The meaning of a symbol cannot be found in its matter, only in the intention/purpose of a mind.
Codons are not ‘symbols’. They are chemicals that correspond to particular amino acids because of the hydrogen-bonding patterns of other chemicals ( tRNAs). The system is redundant and sloppy enough to reject the ‘product of Mind’ hypothesis.
Codons are symbols under any definition of the term.
tRNAs never come in direct contact with amino acids. They need aminoacyl-tRNAs synthase enzymes to join them. There’s no chemical necessity between the amino acid represented and the codon that represent it.
Because codons are symbols, as I said, you can write down your own invented protein sequence in nucleotide language on a piece of paper or in a computer and later have a cell convert it into a protein. Of course that wouldn’t possible if codons were not symbols.
Because codons are symbols, the field of bioinformatics was invented to analyse genomes. There’s a reason why there’s no equivalent to bioinformatics in chemistry or physics. There is no known code occuring outside of biology. Electromagnetism and thermodynamics don’t produce code. If you think it can, go on and make chemistry produce a code, you can win 10 million dollars (see Perry Marshal evolution 2.0 prize).
Maybe the product of a disordered mind? 🙂
@Barbara Knox. Contrary to what ChasCPeterson seems to think, the genetic code is anything but sloppy. On the contrary, analyses of the structure of the code indicate that it is nearly optimal for error minimization! So it must be the product of a very thoughtful, ordered and careful mind !
Which one is the MOST nearly optimal?
https://en.wikipedia.org/wiki/List_of_genetic_codes
There are very minor variations to the standard universal genetic code (which are possible because a code is arbitrary, not the product of any chemical necessity). None of which changes anything to the finding that the genetic code is nearly optimal for error minimization.
Again, if you think that chemistry (electromagnetism and thermodynamics) can produce code how come that no chemical reactions outside of living cells run on code ? How come no one has ever observed chemical reactions starting to produce a code ? Remember, there’s 10 million dollars to win ! Syntax and semantics can only be the product of a mind by definition.
Well I learned something. It seems there is a pretty substantial literature on the supposed optimality of the standard genetic code.
Here’s one example:
https://bmcecolevol.biomedcentral.com/articles/10.1186/s12862-018-1304-0
Pretty interesting stuff, actually. But no Mind is required.
The study you cite is one among a vast litterature. There are many ways one could define and choose to quantify optimality in such a complex system as the genetic code. There’s likely to be in fact many more dimensional axes to consider than the ones that have been included in any given study and many different ways to quantify optimality.
Nevertheless, the litterature considered in its entirety clearly shows that the genetic code is likely near the global optimum if we could include all relevant dimensions (as opposed to a finite subset).
Indeed, the study you cite conclude: “using newly defined quality measures that placed the SGC in the global space of theoretical genetic codes, we showed that the SGC is definitely closer to the codes that minimize the costs of amino acids replacements than those maximizing them.”
But optimality is not the fundamental issue. That’s a distraction. The real issue is syntax and semantics.
“But no Mind is required.”
I’m afraid you’re in denial. This is a metaphysical truth: The meaning of a symbol cannot be found in its matter, only in the intention/purpose of a mind that assigned that meaning to the matter.
The 31 aminoacyl-tRNA synthases — there are only 20 amino acids but there is a tRNA for each of the sense codons — have to each recognize an amino acid at one binding site and a particular region of tRNA, including the anti-codon loop, at the other. The pseudo-doublestranded “cloverleaf” of tRNA has asymmetry that could “help” the synthase recognize the correct region of tRNA as the particular triple-base sequence it must recognize as the anti-codon and not some other trio of sequential unpaired bases. As you imply, only after the tRNA and the amino acid have bound to the synthase (and ATP hydrolyzed) does the synthase form a covalent bond between the carboxyl group of the amino acid and the 3′ end of the tRNA (which is remote from the anti-codon.) This covalent bond will later be broken in the ribosome and replaced with a peptide bond at the end of the growing polypeptide chain.
I don’t see how this is different in principle from any other synthase reaction where the enzyme specifically binds first with one precursor, then (during the time at least some of these enzyme-substrate intermediates last) the enzyme-substrate complex binds specifically with the second precursor and lowers the activation energy enough to make the forward synthesis rate usefully fast. (Since synthetic reactions are typically endergonic, ATP hydrolysis is usually required as well. AA-tRNA synthase is not unique in this regard, either.)
The specificity of making sure that only a tRNA with the correct anti-codon is covalently bound to, say, alanine, resides in there being 31 different synthases. Each one recognizes only one amino acid and it recognizes only one or a small range of anti-codons, the code being degenerate and “wobbly”. But all synthase enzymes have binding specificity for both precursors, not just in protein synthesis. Starting with acetyl-CoA you can make a fatty acid or you can make citrate, depending on whether your synthase currently active is fatty-acid synthase complex (which uses the fatty-acyl chain as its other precursor) or citrate synthase (which uses oxaloacetate as its other precursor.)
Are you making this teleological claim for all synthetic reactions that require two precursors that don’t “know” each other before they are each recognized and “introduced” to each other by the synthase? Or only for aminoacyl-tRNA synthases specifically?
You say further down that other reactions in biochemistry don’t produce “codes”. But the substrate-binding site of all enzymes is “coded for” by DNA. Somehow the genes for the hemoglobin alpha and beta chains have to “know” that the resulting proteins will, when they form a tetramer and complex with iron-heme, create a binding site for oxygen that behaves the right way in the lungs (where it avidly takes up oxygen) and also in the right way in the tissues (where it willingly yields up oxygen to the respiring cells.) To my understanding the precise mechanism by which coding errors (mutations) in the hemoglobin genes cause it not to work properly aren’t known so explicitly as with the AA-tRNAse itself, although the many mutant hemoglobins known offer many clues.
I don’t see anything in AA-tRNAse that cannot be explained by the standard trial-and-error optimization driven by natural selection that everything else in biochemistry follows. Many mutant hemoglobins are incompatible with extrauterine life or they kill affected children in infancy. That is a ruthless natural selection.
Maybe I don’t understand this well enough to grasp the point you are making. I went into some detail (superficial as it may seem) to try to expose where my lack of understanding lies. I am genuinely curious.
(And ChasCPeterson’s 8:30 pm reference is helpful. Thanks.)
JB is the one in denial, insisting a mind must be involved. I wonder what mind he/she could be pondering?? Please demonstrate it JB, rather than asserting it.
I understand the JTF is desperately trying to find a place for a god in the natural world (perhaps at another level, trying to find a place in heaven for JT himself as he must be experiencing the camel and the eye of a needle issue!), but I can’t help seeing their desire for teleology as akin to a child at Piaget’s second stage (the preoperational stage of cognitive development). “The ball fell because it wanted to” etc.
Here is the correct link to the paper by DiFrisco and Gawne: https://academic.oup.com/jeb/article/doi/10.1093/jeb/voae153/7920097