Sunday, 31 August 2014

The great chain of being


Aristotle had the notion that organisms could be placed on a linear natural scale according to complexity of structure and function, such that higher organisms showed greater vitality and ability to move. Evolution has done something similar, building up the ladder of life from very basic micro-organisms and then scaling up to greater integrative complexity. In that sense, living things are concatenations and elaborations of earlier solutions, which have been tweaked through natural selection, refinements being added to the code, often making it a bit longer.

Yesterday a large concatenation of more than 25 authors (did they write a paragraph each?) has published in Nature “Comparative analysis of the transcriptome across distant species” and studied the overlap between humans, worms and flies.

They conclude: Overall, our comparison of the transcriptomes of three phylogenetically distant metazoans highlights fundamental features of transcription conserved across animal phyla. First, there are ancient co-expression modules across organisms, many of which are enriched for developmentally important hourglass genes. These conserved modules have highly coordinated intra-organism expression during the phylotypic stage, but display diversified expression before and after. The expression clustering also aligns developmental stages between worm and fly, revealing shared expression programs between embryogenesis and metamorphosis. Finally, we were able to build a single model that could predict transcription in all three organisms from upstream histone marks using a single set of parameters for both protein-coding genes and non-coding RNAs. Overall, our results underscore the importance of comparing divergent model organisms to human to highlight conserved biological principles (and disentangle them from lineage-specific adaptations).

What has this got to do with our usual subject, intelligence? Well, Heitor Fernandes, Michael A.Woodley and Jan te Nijenhuis have been investigating whether there is a Great Chain of Being Intelligent. Could the same forces that created ancient co-expression modules have done so for the nervous system? Indeed, how could they not have done so? Evolution happens because organisms survive for long enough and in one piece so as to mature and reproduce. They cannot toss forwards only those genes which will conform to refined sensibilities generations later. Do all animals, like humans, have a general intelligence factor accounting for half of their abilities?

As you would expect from these three clever monkeys, the paper is rich with content and deploys some complex statistics. I do not consider myself to be a religious fundamentalist, but this gang even attack principal components analysis. How does one deal with such iconoclasts, who seem bent on replacing the ancient verity with Principal Axis Analysis (see their apostasy below).

Anyway, our three monkeys have respected some traditions in that they evaluate animal intelligence in terms of a Five Factor model of primate IQ: Innovation, tool use, social learning, tactical deception and extractive foraging.

This is what they say:

General intelligence has been shown to exist within and among species of mammals and birds. An important question concerns whether it is the principal source of differences in cognitive abilities between species, as is the case with comparisons involving many human populations. Using meta-analytic databases of ethological observations of cognitive abilities involving 69 primate species, we found that cognitive abilities that load more strongly on a common factor (which is here termed G, in line with the terminology developed in previous literature to describe aggregated measures of general intelligence) are associated with significantly bigger interspecies differences and bigger interspecies variance. Additionally, two novel evolutionary predictions were made: more G-loaded abilities would present (1) weaker phylogenetic signals, indicating less phylogenetic conservativeness, and (2) faster rates of trait evolution, as it was hypothesized that G has been subjected to stronger selection pressures than narrower, more domain-specific abilities. These predictions were corroborated with phylogenetic comparative methods, with stronger effects among catarrhines (apes and Old World monkeys) than within the entire primate order. These data strongly suggest that G is the principal locus of selection in the macroevolution of primate intelligence. Implications for the understanding of population differences in cognitive abilities among human populations and for the theory of massive modularity applied to intelligence are discussed.

We obtained meta-analytical frequency-count data on five cognitive abilities from a total of 69 primate species. Data on four different cognitive abilities were obtained directly from Reader et al. (2011). Their meta-analytic database was produced by examining over 4000 articles published from 1925 to 2000 for reports of behaviors indicative of intelligence (described above) in extant primate species. Data on a fifth cognitive ability were obtained from a meta-analytic compilation produced by Byrne and Whiten (1990), and originally obtained by surveying the large memberships of the International Primatological Society, the Primate Society of Great Britain, the Association for the Study of Animal Behavior, the Animal Behavior Society, and the American Primatological Society combined.

Different species use complex problem-solving behaviors in different ecologies, thus the various senses (e.g., olfaction, hearing) have different weights of importance for different species with regard to how they perceive and identify ecological and social problems to be tackled, the motivation systems, dependence on rewards, and tolerance to frustration vary across species, thus it is extremely difficult to calibrate experimental conditions to the ecological idiosyncrasies of each species.
Additionally, experimental cognitive tests are not available for large numbers of species or on a sufficiently broad range of cognitive abilities. Hence the natural frequency-counts approach used in the collection of the current dataset is the most
appropriate and ecologically valid estimate of intelligence for comparative studies, that is, studies in which macro evolutionary predictions are being tested at the cross-species level (Reader & Laland, 2002; Reader et al., 2011; see also Lefebvre, 2011).

We conducted a Principal Axis Factor analysis (which, contrary to principal components analysis, controls for error variance; Costello & Osborne, 2005) to test the factor structure of the five cognitive abilities. We also tested their factor structure with Unit Weighted Factoring (UWF), which avoids the well-known sample-specificity of factor-scoring coefficients produced by standard errors of inconsistent magnitudes in small samples (Gorsuch, 1983). Both factor analyses were conducted after residualizing each cognitive ability against research effort so as to avoid publication bias.

The findings reported here have substantial implications. Firstly, the species differences in intelligence and their variance from the mean are biggest on the more G-loaded cognitive abilities, as is also the case for population differences within the
human species. This suggests that the evolutionary accounts developed to explain population cognitive differences in humans are plausible, as it is improbable that a “Factor X” (the term generally used to refer to putative environmental
causes of population differences in cognitive abilities; Jensen, 1973) could be operating to create the findings reported here among primate species. Several putative “Factor Xs” involve systematic negative discrimination or stereotype threat
(Sesardic, 2005). It is difficult to envisage how these social forces might extend across primate phylogenies. A more parsimonious account of the apparent ubiquity of validation for Spearman's hypothesis is that it results from more common-factor-loaded abilities simply being more revealing of taxonomic group differences owing to differential selection having operated historically on general intelligence to a greater extent than on narrower and more modular abilities — and that this is likely the same for human populations as it is for primate species, the principal difference being the duration of selection.

Comment: it looks as if a G factor (principal axis based on aggregated measures) can be extracted from primates, even though they cannot be tested with pencil and paper and spoken vocabulary definitions. Primates appear to conform to the same general intellectual factor g (based on individual measures) which underlies human abilities.

Darwin should have the last word (1871, p. 105)

“the difference in mind between man and the higher animals… is certainly one of degree and not of kind" (Italics added for emphasis).


  1. Professor Thompson,

    My apologies, I know this is off topic but I think this is an important article:

    "One of the great errors of an elite education, then, is that it teaches you to think that measures of intelligence and academic achievement are measures of value in some moral or metaphysical sense. But they’re not. Graduates of elite schools are not more valuable than stupid people, or talentless people, or even lazy people. Their pain does not hurt more. Their souls do not weigh more"

    Read the whole here:

    1. "By nature all men are equal in liberty, but not in other endowments". As Aquinas observed, we accord equal liberty to all citizens, as part of an altruistic assumption, hoping to get the best out of them, and out of society. Nonetheless, profound differences remain. So, your Ivy League graduate need not be more moral, or of higher personal value in a metaphysical sense. They will certainly be very very likely to be of more financial value, and that has positive moral implications because taxes on them will support other families. In fact, they are also a bit more likely to be tolerant and socially involved, and thus good people. As to the article, it pulls together a whole lot of different effects and attributes it to elite university education. I think the observed differences are not primarily due to education but to prior differences in interests. Final disclosure: I have no difficulty talking to plumbers, and painters. The guy painting for us at the moment only does so for clients who provide references to him. He does not like ill tempered customers, or those who quibble about his moderate bills.

    2. Mr. Thompson,

      Do you have sympathy for intellectually slow people?

      Let me clarify what I mean by ‘intellectually slow person’. Obviously I am not referring to the person who meets the criteria for an Intellectual Disability (also called mental retardation)…. I am talking about the person who has the ability to learn necessary academic skills, but at a rate and depth below average same age peers. In order to grasp new concepts, this person needs more time, more repetition, and often more resources from teachers to be successful. Typically, this person has great difficulty with new and complex reasoning which makes new concepts difficult to learn.

      A slow learner has traditionally been identified as anyone with a Full Scale IQ one standard deviation below the mean but not as low as two standard deviations below the mean. The cognitive abilities of these learners are too high to be considered for an Intellectual Disability. However, the abilities are usually too low to be considered for a Learning Disability. Consider that a learning disability consists of discrepancies between average abilities and below average academics, coupled with a processing deficit. Schools often look for a discrepancy between a student’s ability and where they are performing. Slow learners tend to perform at their ability level which is below average. Unfortunately, these struggling learners often do not receive special education services.

      These individuals are prone to much anxiety and low self image which goes unnoticed by many in society. They often feel ‘stupid’ and begin hating school at an early age. Day-to-day academic life can be very draining and yet many somehow manage to make it through the system and through high school (in the United States)

      The psychologist and intelligence researcher Linda Gottfredson wrote a good piece titled Why g Matters: The Complexity of Everyday Life. An excerpt:

      “Life is replete with uncertainty, change, confusion, and misinformation, sometimes minor and at times massive. From birth to death, life continually requires us to master abstractions, solve problems, draw inferences, and make judgments on the basis of inadequate information. Such demands may be especially intense in school, but they hardly cease when one walks out the school door…”…prints/1997whygmatters.pdf

      Two questions:

      1. Can you sympathize with a person who says that one of their major reasons for contemplating suicide often is that they just don’t feel competent to handle the mental demands of today’s increasingly complex social environment?

      2. Is it morally permissible for the intellectually slow person to commit suicide?

    3. Thanks for your question. Due to my own incompetence, the first draft of my reply to you has been lost, so I certainly have sympathy for those who don’t feel competent to handle the mental demands of today’s increasingly complex social environment. Remember, that is not just IQ, but also part of ageing.
      I am a big fan of Linda Gottfredson's work. Put her name into the search bar of my blog and you will find about 30 references to her.The one below takes up the same reference you kindly gave in your comments.
      As to suicide, it would be dreadful if someone ended their life because they felt incapable. I feel sympathy with anyone in that predicament, and because I often meet people who are much brighter than I am, and who are much more dedicated to their work, I certainly think I know what it is like to feel slow intellectually. Morally permissible? I don't agree with that. Terminal illness and pain would be a good reason, but being a slower learner definitely not. Depending on the company we keep, most of us can be considered slow.

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  3. different species are decent solutions for their varying ancestral environments.

    not sure how my chipmunk knows when to "torpor," or how bees know how to interact with their sisters, or how spiders determine if there's enough moisture to hatch, or how water bears can do "cryptobiosis" for years then "come alive" when the time is right.

    i don't think these things are "g" related, so i agree with Gould (on this & this only), it's difficult to establish a great chain of being b/c "g" only works that way for primates:)

    PS - in re: to comment above -- given the high predisposition of older white males to commit suicide, i would think most successful suicides have triple digit IQs. i also think it should be legal (both to be smart & to be the boss of your life:)

  4. Need to post on encephalisation and intellect. Smart birds have bigger brains than other birds. g holds true for humans, primates, and probably dogs. Rosalind Arden is looking for funding to get more dog intelligence work done on larger samples.

    1. If g holds true for other species (dogs,birds), does that imply co-evolution or will the infancy for g be located in a common ancestor species?

    2. I think we can show co-evolution with dogs, which is why we imagine we understand each other, but not birds and not most living things. As to common ancestor species, I think that is closer to the case, but only because all organisms have common problems to solve: finding food and avoiding predators. That requires a nervous system of some sort, and what we call intelligence arises from that. Wisner-Gross would say that it was an emergent property of all complex systems which have to avoid getting trapped by keeping their options as open as possible. F = T ∇ Sτ is the formula.

    3. Fascinating!
      It seems so simple and straightforward that I fear I must be mis-understanding it.
      Recognize the greatest number of options and conform your behavior to maintain the viability of the greatest number of these options into the future. Repeat for a few hundred million years.
      This segues into what we know about ourselves today. Higher ability people are better at handling adversity and changed circumstances that are lower ability people.

    4. It is a fascinating proposal. I have put it into my overflowing "Must post more about this" in tray.

    5. This is my first mention of it.

  5. Professor Thompson

    You have one of the best blogs that I have happened upon. Please keep up the good work.

    It seems that a lot of people have a great deal of difficulty handling the fact that some people are just a lot smarter than others.

    One thing that has been in my mind for a long time is the following:

    I was told that supposedly there are tasks/jobs at which lower IQ people are better at than higher IQ people. Some high IQ types thought that this could not possibly be true and did some studies. Supposedly they found out that at what might be considered boring tasks, the high IQ minds wandered and made more mistakes. Also, the low IQ types took as gospel that an error or mistake was a near catastrophe whereas the high IQ types could see that a mistake was really not all that bad so they did not work as hard at avoiding them.

    Do you know of any such studies? Or was I perhaps just being mis-lead for my own good.

    And along that same line, don't you think people should quit kicking the corpse of poor ole S J Gould. I mean, if you are not willing to lie for the betterment of mankind, just what kind of person are you?

  6. I don't know of any studies showing that low ability people do better at boring tasks than bright people. Most findings are to the contrary: high ability people are better and faster at all tasks. I think the misunderstanding arises because bright people generally don't stick at boring work, so some employers prefer to hire lower ability workers who will probably remain in the job longer. Some data from the London Underground decades ago showed that the slower learners stuck the not very appealing job for years on end. True, they also had fewer job opportunities. (Now, to confuse matters, they have very high earnings because of strong unions).
    Stephen Jay Gould. He had a very good prose style. I wish he had been more even handed and straightforward in talking about intelligence, and corrected his errors sooner, but that is paperbacks under the bridge. Thanks for your comments.

    1. Thank you.

      Maybe a fallacy could be named for him. That would make it better.

  7. The Gould cranial fallacy? Gouldian plausibility?

  8. PCA is conceptually distinct from exploratory factor analysis. It incorporates all variance into the analysis and does not discriminate between common and unique (error) variance, whereas EFA assumes that each variable is a linear function of a unique factor and 1 or more common factor(s), and attempts to model the relationships between common factors and their relationships to the actual variables.

    The upshot of this is that although PCA and EFA usually produce similar results, only factors should be thought of as latent variables, not components. It's a philosophical difference that is sometimes important.

  9. The Gould Proposition

    It is not immoral to fudge the numbers if the motivation to do so abides by the greatest good principle.

  10. If the concept of g factor either state universal characteristics that define the intelligence, I can agree. But I can not agree that the g factor is universally applicable.
    Your concept is, but its reachability is limited.
    Yes, there is a clear relationship between mathematical reasoning and verbal reasoning. However, the fact that there is a correlation, it is not conclusive as to its universal applicability.

    Another problem is that for intelligence is attributed unilateral judgment of value among the cognitive characteristics. For example, people of low intelligence, are considered as hopelessly inferior to people of higher intelligence, read iq, when it is clear that if you have a lack of any component, you will get the compensation. Brains do not have voids inside, I guess. There many other advantages related not only with cognitive capacity but, general capacity, like psychological advantages.

    I still believe that a good portion of psychometry, still based on the idealization of what intelligence is, while it is a universal value, literally. And the best way to understand it is through the ability that people have to find harmonic and disharmonic patterns in the real world.
    If you are able to find the correct causal patterns, then you may be able to understand the reality and to infer more complex abstract observations.

    The 'Education' is a filter, derived from the ancient Chinese meritocracy. The memorization capacity is the star of education and those who can decorate a larger amount of information, will be more apt to go up in scale, social and academic. However, there are so many environmental factors (nepotism, favoritism by cognitively non-objective reasons, unilateral selection of a type of intelligence for colleges ..) we are being deceived by our faith in the meritocracy of Western civilization, which have long been deteriorated.

    We're defining 'smarter' based on the results of all these factors. Not only are we defining mistakenly 'smarter' but neglecting the diversity of 'smarter' based on unilateral selective filters as iq and 'education'.
    Another mystery of psychometrics is the way psychometricians take iq tests. There are no criteria in conducting research, speak iq without specifying what iq is working, finally ...