Explanations and Bad Science

Explanations are wonderful things. They provide the world around us with meaning, a way of reasoning with others and a path to understanding scientific processes. Explanations may also sow the seeds of bad science.

Bad Science can be interpreted in a number of ways. The media and “science” journalists interpret “bad” science to mean anti-science or “science” conducted by non-scientists, based on results that are corrupted, forged or spurious. We believe however that bad science is nothing more than “made-up-ology”, which is created by scientists in order to make highly speculative claims to explain natural phenomena. Strangely the media never pick up on our version of bad science, possibly because “science” journalists are there to report positively about science rather than to criticize scientific explanations.

Anyone with enough qualification to report on scientific endeavor has the ability to see through spurious claims, reconstructions or theories. Dinosaur reconstructions based on a single jaw fragments for instance, rate highly in our list of bad science. There are limits to reconstructions, many of which never see the light of day in scientific journals but feature on the cover of “scientific” magazines. The aim of such reconstructions apparently are to to communicate a predicted past event, such a meteorite impact, to a popular audience. The idea is analogous to comparing a period-dress Hollywood blockbuster to an actual historical event. The event most likely occurred, but since it was not recorded in detail nor witness by anyone living, still remains unknown. Discovering a dinosaur jaw or even complete skull does not mean we can determine its size or colour; reconstructions and films based on “true events”, the actual machinations, are fictitious. Reconstructions however are powerful ways to explain important events.

The Power of Explanation

Explanations are mechanical devices with which to predict or retrodict future or past events and processes that are unobservable. Most important is that explanations rely on discoveries.

In experimental science, such as chemistry, phenomena are observable and repeatable. We may discover for instance that two chemicals added together produce another. The event can be repeated, described and observed, therefore resulting in an explanation of the processes involved. Non-experimental sciences such as palaeontology however rely on retrodictions based on evidence to hand. The discovery of a fossil jaw bone for example, is limited to description and observation of its form. The processes that the jaw bone underwent when it was part of a living creature are unobservable and not repeatable. The resulting explanations are quite different from those in chemistry as they are based on assumptions, theories, hypotheses and comparisons. In palaeontology we choose the best explanation based on the most convincing and rational argument. That argument is tied to accepted theories and hypotheses at the time meaning that explanations are forever changing and ephemeral. This does not mean that non-experimental sciences like palaeontology are bad or non-scientific. Many scientific fields that involve the study of past events are far more reliant on patterns than the experimental sciences (i.e., ecology, systematics, biogeography, geology, geography). Explanation, it seems, provides greater meaning.

The non-experimental sciences are primarily descriptive and comparative, relying on form and its relationship rather than on explanations. Given that normal processes are taken for granted in the experimental sciences (i.e. photosynthesis, digestion, ontogeny etc.), they are not evident in the non-experimental fields. Without the luxury of observing processes, scientists are reduced to making up hypothetical explanations in order to provide some kind of meaning. This is understandable in a world where explanations are seen to be more meaningful that form. For us form, its description and comparison, is meaningful. The discovery of patterns and relationships between form is possibly the most powerful scientific endevour. Without it we live in the present with no knowledge of the past. Many scientists within palaeontology, geology, systematics and biogeography feel that the discovery of relationship is not enough. The rise of hypothetical mechanical explanations as “meaningful” is where we believe bad science to begin.

Divisions: Who watches the philosophers of science?

There are a few things for the poor old philosophers of science to get over.

If Peter Lipton is right, namely that,

"Astronomers study the stars; philosophers of science study the astronomers. That is, philosophers of science—along with historians and sociologists of science—are in the business of trying to account for how science works and what it achieves" (Lipton, 2005: 1259).

then philosophers of science have to able to see beyond current trends and political avarice. After all who watches the philosophers of science?

The trend of embracing apparent dichotomies within systematics and biogeography rather than question them, is one of things that philosophers of science need to get over. Philosophers of science need to question, examine and assess such divisions and not blindly accept them as many seem to do.

Below we list the top 10 dichotomies in systematics and biogeography that philosophers of science need to get over:

1. Morphology and Molecules
2. Homology and analogy
3. Homology and homoplasy
4. Transformational and Taxic Homology
5. Synapomorphy and symplesiomorphy
6. Congruence and consensus
7. Cladistics and Phenetics
8. Simultaneous analysis and separate analysis
9. Ecological and Historical Biogeography
10. Dispersal and Vicariance

Just because scientists use these divisions does not mean they actually exist. Dichotomies often groups "us" from "them". Science is not immune from subjectivity or distortion of "the facts" through clever manipulation. Scientific decisions too are sometimes decided upon politics, personality and fashion.

Philosophers of science are there to make sure that fish caught last Sunday afternoon was indeed "that big". In believing, rather than questioning, the divisions between certain ideas that are made by scientists, philosophers of science are unable to for "account for how science works". For some philosophers of science, the one that got away was "ooh .. so big, bigger than anything you have ever seen".

Lipton concludes

"Indeed, one might go so far as to worry that if philosophy did have any impact on scientists, it would be pernicious, depriving them of the kinds of commitment and confidence upon which their practice depends" (Lipton, 2005: 1269).

Philosophers of science have already influenced science, based on some of the highly questionable divisions listed above, to the extent that that it has been fashionable to attribute the cladistics/phenetics "war" in systematics to real events rather than to a poor account of how science functions (i.e., Hull, 1988).

References
Hull, D.L. 1988. Science as Process: An Evolutionary Account of the Social and Conceptual Development of Science. Chicago: University of Chicago Press.
Lipton, P. 2005. The Medawar Lecture 2004: The truth about science. Philosophical Transactions of the Royal Society of London B, 360, 1259–1269.

Buddah: Look at the moon, not my finger!

Joe Felsenstein has suggested an analytical example, one he felt we might like to examine. The example is simple:

"If we take a sequence alignment, perhaps an easy case such as an alignment of exon sequences of a gene, and then we run (say) a parsimony algorithm, and consider ourselves to be making an estimate of the unrooted evolutionary tree (perhaps later rooting it by outgroup), what do Ebach and Williams say of this?"(Felsenstein in Comments)

Felsenstein kindly offers a few suggestions ("guesses") as to what we might think. These are as follows::

1. It is not inferring the phylogeny because this process is "phenetic"


2. It is not making a classification so it is fine but not of interest to us


3. It should instead be trying to make a classification


4. It is making a classification but a "phenetic" one so not a good one.

Felsenstein offers a view as to which of the suggestions ("guesses") is correct, opting for number 4: 'It is making a classification but a "phenetic" one so not a good one'.

Of course, we welcome helpful suggestions ("guesses"), as our desire has been (and hopefully will remain) the examination of the process of systematics, a complex field that develops and grows, as does all science. Thus, we crave his indulgence at our dissection of his suggestions in the interest of scientific endeavour.

First, we find it a little troublesome to deal with efforts that are thought ‘good’ or "bad" and do not really know what those words might mean in the context above. To us, phenetics is neither good nor bad. Consider the following. Linnaeus created the Sexual System of classification for plants, a system he acknowledged as artificial. That system still has its uses, when one is faced with a particular plant and needs to know its name, then (usually) that can achieved by working through the Sexual System. It is an Artificial Classification – it is neither bad nor good (Linnaeus knew that). It is inappropriate when wishing to investigate the natural system; it is appropriate when wishing to find a name.

Second, whether one is "inferring the phylogeny" or just exploring the distribution of homologies, any branching diagram that results can be made into a classification. Thus, points 1—4 above are without meaning.

In our (several) posts we noted that Natural Classification is investigated using homologies – and similarities, in and of themselves, are not homologies. Consider a matrix of characters, with either 1's and 0's or A's and T's ("…take a sequence alignment…"). What are they? Similarities. The matrix is, one might say, phenetic. The application of UPGMA, or Neighbor-joining, or parsimony, or…well, whatever, cannot change that fact. And, it would appear, that UPGMA, or Neighbor-joining, or parsimony, and so on, are all forms of weighting, regardless of whether one might believe that the 'model' is an accurate representation of the evolutionary process. Now as we noted, "Phenetics uses a method in order to generate a classification that mimics a natural group. The method for doing so can be useful in order to work out similarities between taxa, but the method is only a mimic." Thus, we might offer the following: much of the last 40 years of exploration of methods has, inadvertently, focused on ways one might modify or adjust a matrix of similarities.

We do not have, nor do we promote, any "favorite approach…". This is not a competition. Systematics (classification, phylogeny) is about homologies and their distribution.

The cladistic revolution of the 1960s was necessary because of palaeontology, its promises, its claims, and what it delivered. Palaeontology is reformed as a consequence, yet its effect on systematics, mostly detrimental, lasted 100 years.

Perhaps it's time for another revolution.

Wag the Dog: Mimics, False Prophets and Phenetics

Near enough is not good enough should be the motto of cladistics. For many however, near enough is not only better, but something worth pursuing. Phenetics is that "something". It is a mimic and some of its proponents are false prophets who prefer a "near enough" result to a real understanding. Systematics and biogeography can not rest on its numerical laurels too long. Already in molecular systematics the numerical method is defining the field. When the mimic starts to dictate what the science should be, we have a severe case of the dog’s tail wagging the dog.

Mimics

Artificial classifications are a key or classification based on a particular organ. This forms a System, one that can predict or mimic a natural classification.

Taxonomists, systematists and biogeographers often use artificial classifications or Classification Systems in order to identify and classify taxa. People around the world use classification systems everyday. This is one that many learn at school:

1. Fish have scales and no limbs.
2. Amphibians lay eggs on land and live in water.
3. Reptiles lay eggs, have scales and live on land.
4. Birds lay eggs and have feathers.
5. Mammals have skin and hair, mothers feed their young milk.

Classification systems are helpful in identifying taxa but they only mimic real relationships. In the case above only mammals and birds are natural (monophyletic) groups, but the classification system for birds may also apply to taxa that are categorized as reptiles. In other words, the system above only mimics the natural group (i.e., birds), but it does use the homologies that define that group.

Linnaeus was the first person to define a classification system that attempts to mimic natural groups. The system can still be used today in order to identify plants. What Linnaeus’s, or any classification, does not do is purport to be a natural method.

A method is a key or classification based on all of the organs of a taxon; methods are sub-divided into artificial and natural depending on their purpose.

Classification methods not only mimic, they also may predict. In either case they attempt to generate classifications that are near the mark. Phenetics uses a method in order to generate a classification that mimics a natural group. The method for doing so can be useful in order to work out similarities between taxa, but the method is only a mimic. Phenetics becomes problematic when it starts getting closer to the mark. In some cases a phenetic analysis can replicate a true relationship – a homology – without the need for homologies. Although these methods are praiseworthy, they do not actually find homologies. A mimic only replicates something, it does not actually discover. A phenetic analysis may for instance replicate a monophyletic group perfectly, using an assortment of homologues, but since the method uses similarity (i.e., non-relationships) it cannot, by definition, discover homologies, even though it replicates them perfectly.

An analogy would be to state that anything that lives in water and lays eggs on land is an amphibian. Although this behavioural trait is more likely to be common amongst toads, frogs, salamanders and newts, it is not a homology as it is something not unique to that group. Birds may lay eggs and bear feathers, but so do a number of therapod groups. Similarity is not a relationship, only a measurement of likeness based on one or more hypotheses.

False Prophets

Phenetics becomes problematic when it confuses the mimic for the real thing. Certainly phenetics can create a classification system using a method of similarity, but it does not discover natural groups. Therefore the term Natural System is a contradiction. A system cannot be natural as it is based on a single characteristic or assumption and not relationship. Natural groups, as pointed out in the post Phenetic "Natural" Classifications, are not based on a priori assumption:

"... system of classification is the more natural the more propositions there are that can be made regarding its constituent classes" (Sokal & Sneath 1963: 19).

Sokal and Sneath (1963) have turned the mimic into natural group.

Phenetics as purveyor of natural groups is erroneous and prophetic. Stating that natural groups can be reached through a system of quantification and similarity is appealing to those that rely on statistical programs. Most systematists and biogeographers rely on such programs and have swallowed the “phenetic prophesy” hook, line and sinker. Natural groups, it seems, is just a matter of quantity.

Wag the Dog

The phenetic prophesy states that similarity* is relationship, and can discover natural groups. This is wagging the dog.

Taxonomists, systematists and biogeographers can only discover patterns, homologies that give us insight into relationship. Before we do this we may impose a system of beliefs, hypotheses and theories about our own groups and their relationships. Some times we test these assumptions by discovering homologies and find that we were right. That is the nature of a robust scientific discipline. Once we turn that around and impose our own “natural” law, then we can only formulate more hypotheses in differing ways, never discovering only generating. Molecular systematics is now in a unique position to learn from 300 years of systematic theory that has discovered time and time again that homology is not similarity. Unfortunately many in the field ignore the past systematic literature and read that of the phenetic prophesy.

One day someone bent over a PCR machine may come to realise that they are part of a 300 year cycle of wagging.

*There are two forms of similarity. One is that of simile “That kangaroo looks like a rat”. The other is quantifiable and is born from statistics (i.e., divergence and possibility) “The ape is 22% banana”. We refer to the latter form throughout this post.

References

Sokal R.R. & Sneath P.H.A. 1963. Principles of Numerical Taxonomy. W. H. Freeman, San Francisco.

Natural and Artificial Classification: A reply to Wilkins

The following post is a reply to John Wilkin’s The philosophy of classification on his blog Evolving Thoughts.

An Uninformed Consensus

John Wilkins in his recent post believe that our view is "radical" because

"… they have presented some views on classification that do, indeed, differ from the received consensus."

We beg to differ.

In late 20th and early 21st century literature there are very few discussions on the nature of classification. Most revolves around explaining existing classifications (i.e. Reptilia) or in the defence of poorly defined taxonomic groups that fail to form groups (i.e., paraphly). It is these debates (i.e., paraphly versus monophyly) that would benefit from the discussions of early 20th and late 19th century morphologists, would did hold a consensus view of natural and artificial classifications. That consensus was this,

We then follow a Natural Method, which cannot be called a system, because it is destitute of any unity of principle. (Candolle & Sprengel, 1821)

It is our belief that the pursuit for explanations to existing classifications that ended this debate and therefore any consensus. Furthermore, it is the addition of homology = similarity that radically altered how we view classifications, leading to the almost Fukuyamaist statement that,

"I would say that the effort put into this controversy is further evidence that systematists do not have their priorities straight. In their day-to-day work they really do not make much use of classifications, but they show a strange obsession with fighting about them for reasons that seem to me to be an historical curiosity" (Felsenstein 2005)

Currently there is no consensus over natural or artificial classifications. The topic is a moot point and very few concern themselves with its relevance to 21st systematics and biogeography. As systematists we are more or less tied to the consensus of the past, namely to the literature of the 19th century and early 20th century. In that sense we are not “radicals", but rather “old fashioned”.

Similarity and Homology

Similarity, as expressed in the usual kinds of data matrices, is 11, or, the molecular version, AA is not a relation. The 11 and the AA are, if anything, homologues, the parts, the 'namesakes' as Owen called them. We see homology as a relation: 0(11), or the molecular version, G(AA). We stated earlier:

"...all molecular systematic studies are phenetic as they ignore relationship, that is, homology". One might expand that and say, "...all numerical systematic studies are phenetic as they ignore relationship, that is, homology."

This would be more accurate.

In response to John’s comment,

"I'm not sure I follow this. According to current usage, molecular systematics does rely on homologies: they have a number of special terms devoted to identifying them: paralogy, xenology and orthology. Of course, they often don't use homology properly. And to identify a homology in molecular biology you need to do some prior work; homology is an inference from sequence similarity (including eyeball alignment). In short, if I understand the argument, molecular systematics derives homology from similarity".

In fact we would suggest that it would be more accurate to say:

"... molecular systematics does rely on HOMOLOGUES: they have a number of RELATIONS DERIVED FROM them: paralogy, xenology and orthology....And to identify a HOMOLOGUE in molecular biology you need to do some prior work; HOMOLOGUES ARE inferenceS from sequence similarity (including eyeball alignment). In short, if I understand the argument, molecular systematics derives HOMOLOGUES from similarity ..."

This certainly is not radical. What we are suggesting is that de Candolle (1813) presented a very clear account of classification, an account still of significance today.

Haeckel and Classification

In our understanding, Ernst Haeckel did more than most to promote the genealogical view of species relationships. It might be fair to say that all our genealogical endeavours stem from Haeckel. Adolf Naef (1917, 1919)was the first to critique that viewpoint His interest was in natural classification. Hennig (1950), quite deliberately, focused on Naef. Thus, it might be fair to say that Hennig's efforts were directed towards rehabilitating Haeckel. Further, one might see Systematics and Biogeography (Nelson & Platnick, 1981) as a further detailed critique of Haeckel - if the most detailed critique available - and a restatement of de Candolle's viewpoints on classification. In this sense cladistics sensu Nelson & Platnick is of greater significance than cladistics sensu computer programs.

We would venture the suggestion that Sober (1988) mistook cladistics sensu Farris (parsimony sensu Farris) as if it was the generally accepted view (in the mid-1980s that might have been possible). In fact Sober deliberately excludes the more general view, as if the argument really was about parsimony versus likelihood, one algorithm versus another,

"Because this work is about phylogenetic inference, not classification, nothing will be said about the current controversy concerning so-called 'pattern' cladism." (Sober, 1988:8, footnote 7).

Thus, in our view, the more general study of classification exclude Sober's work as a relevant commentary on the matter.

References
Candolle, A.P., de, & Sprengel, K. 1978. Elements of the philosophy of plants. Reprint of the 1821 ed.. New York, NY.
Hennig, W. 1950. Grundzüge einer Theorie der phylogenetischen Systematik, Deutsche Zentralverlag, Berlin.
Naef, A. 1917. Die individuelle Entwicklung organischer Formen als Urkunde ihrer Stammesgeschichte: (Kritische Betrachtungen über das sogenannte "biogenetische Grundgesetz"), Verlag von Gustav Fischer, Jena.
Naef, A. 1919. Idealistische Morphologie und Phylogenetik (zur Methodik der systematischen), Verlag von Gustav Fischer, Jena).
Nelson, G. & Platnick, N.I. 1981. Systematics and biogeography. Cladistics and vicariance. Columbia University Press, New York.
Sober, E. 1988. Reconstructing the Past: Parsimony, Evolution, and Inference. MIT Press, Cambridge, Massachusetts.

Artificial and Natural Classifications: A Clarification

It was not by accident that we referred to de Candolle (1813): "Naef's concern was with the discovery of natural, as opposed to artificial classification, a problem examined in detail by A. P. de Candolle (1813)".

This is what de Candolle had to say about artificial classifications:

"Others have as their essential goal to give to persons who know nothing of the names of plants an easy way to discover the names in the books by inspection of the plant itself. These classifications have been given the name of Artificial Methods."

And,

"...there are those persons who want to study plants, either in themselves, or in their real relations among themselves, and to class them so that those plants most closely related in the order of nature are also those most closely related in our books. These classifications have received the name of Natural Methods."

De Candolle considers Systems and Methods.

A system is a key or classification based on a particular organ - leaf, flower, etc.

A method is a key or classification based on all of the organs of a plant; methods are sub-divided into artificial and natural depending on their purpose.

De Candolle again:

"classes that are truly natural, established on the basis of one of the major functions, are necessarily the same as those established on the basis of the other."

That is, congruence.

Bar-coding, based on "a particular organ", interpreted as a piece of DNA, is, in this sense, a system. It might be seen as an artificial classification as its purpose is to find the name of any given plant or animal.

Now, is molecular systematics a system or a method? It too is based upon "a particular organ", so it too might be considered a system. Now if considered a method, we see that there is no notion of congruence at all as no other datasets are given consideration. Molecular systematics as a form of measuring similarity constitutes a system, not a method.

Ancestors and other mechanical explanations are not of any concern in the debate between artificial and natural classifications. One does not decide on homology in advance. It is either there or it is not. Homology, as we understand, is a relation. A similarity such as 11, or AA, is not a relation. Thus, all molecular systematic studies are phenetic as they ignore relationship, that is, homology.

Adolf Naef - A Potted Biography

Who was he?
Adolf Naef was a Swiss systematist, malacologist and a proponent of systematic morphology. He was born in Niederhelfenschwil on 1st May 1883 and passed away on May 11th 1949.

What did he do?
Naef studied at the University of Zurich, under the guidance of Arnold Lang (1855—1914), a former Professor of Jena University and close friend of Ernst Haeckel. Naef visited and worked in Anton Dorn’s Zoological Station in Naples, Italy in 1908, studying the squid Loligo vulgaris, the subject of his dissertation (Naef, 1909a, b). Naef returned to the Naples Zoological Station in the mid 1920s to study cephalopods, publishing a two-part monograph in the Station’s Fauna und Flora des Golfes von Neapel und der Angrenzenden Meers-Abschitte (Fauna e Flora del Golfo di Napoli) series (Naef 1921d, 1923c, 1928, later translated into English, Naef, 1972a, 1972b, 2000), which formed the basis for his two short but significant monographs on systematic theory (Naef, 1917, 1919). In 1922 he became Professor at the University of Zagreb, and in 1927 was Professor of Zoology at the University of Cairo.

What’s the big idea?
Naef’s studies were framed within Systematische Morphologie (Systematic morphology) (Naef, 1917, 1919), the details he sketched out as early as 1913:

“Phylogenetic and natural systematics deal with the same factual material, and although each has different basic concepts, both disciplines can be united in a single concept because their objects are so similar. I have therefore proposed the name ‘systematic morphology’ for this concept (Naef, 1913: 344)…It is intended to show that there is an inner relationship between natural systematics and (comparative) morphology” (Naef, 1921-23: 7, from the English translation, Naef, 1972a: 12).

Naef’s concern was with the discovery of natural, as opposed to artificial classification, a problem examined in detail by A. P. de Candolle (1813). Naef expressed it as so:

“For decades, phylogenetics lacked a valid methodological basis and developed on the decayed trunk of a withering tradition rooted in the idealistic morphology and the systematics of pre-Darwinian times. There was talk of systematic ‘tact’ and morphological ‘instinct’, terms which were felt rather than understood and consequently insufficient to form the frame of a science which required sound definitions and clearly formulated principles” (Naef, 1921-23, pp. 6-7, from the English translation, Naef, 1972, p. 12).

And thus was born ‘Systematische Morphologie’, perhaps the beginnings of cladistics, in its most general form (of which more in a further post). Towards the end of his career, Naef published several detailed accounts of ‘Systematische Morphologie’ (Naef, 1931a, b, 1933a), including a succinct summary in the widely read 2nd edition of the Handwörterbuch der Naturwissenschaften (Naef, 1933b).

Naef might be considered a man out of time – as might many morphologists today, relative to the explosion of molecular data. In Naef’s day palaeontology and the post World War II hegemony of the modern synthesis was attracting the young minds. Today it is molecular systematics and DNA barcoding – versions of artificial classifications.

References

Candolle, A.-P. de (1813). Théorie élémentaire de la botanique ou exposition des principes de la classification naturelle et de l'art de décrire et d'étudier les végétaux. Deterville, Paris.
Naef, A. (1909a). Die Organogenese des Cölomsystems und der zentralen Blutgefässe von Loligo. Jenaische Zeitschrift für Naturwissenschaft, 45, N.F. 38:221—266.
Naef, A. (1909b). Die Organogenese des Cölomsystems und der zentralen Blutgefässe von Loligo. Inaugural-Dissertation, Univers. Zurich, 46pp.
Naef, A. (1913). Studien zur generellen Morphologie der Mollusken. 2. Teil. Das Cölomsystem in seinen topographischen Berziehungen. Ergebnisse und Fortschritte der Zoologie 3: 329—462.
Naef, A. (1917). Die individuelle Entwicklung organischer Formen als Urkunde ihrer Stammesgeschichte: (Kritische Betrachtungen über das sogenannte “biogenetische Grundgesetz”). Verlag von Gustav Fischer, Jena.
Naef, A. (1919). Idealistische Morphologie und Phylogenetik (zur Methodik der systematischen). Verlag von Gustav Fischer, Jena.
Naef, A. (1921—23). Die Cephalopoden (Systematik). In: Fauna e Flora del Golfo di Napoli, Monograph 35 (I-1), Pubblicazioni della Stazione Zoologica di Napoli. R. Friedländer and Sohn, Berlin, pp. 1—863.
Naef, A. 1931a. Allgemeine Morphologie. I. Die Gestalt als Begriff und Idee, pp. 77—118 in Bolk, L, Göppert, E., Kallius, E. & Lubosch, W., (editors) Handbuch der vergleichenden Anatomie der Wirbeltiere 1. Berlin: Urban & Schwarzenberg.
Naef, A. 1931b. Phylogenie der Tiere, pp. 1—200 in Baur, E., & Hartmann, M., (editors) Handbuch der Vererbungswissenschaft, Gebrüder Borntraeger, Berlin 13 (3i).
Naef, A. 1933a. Die Vorstufen der Menschwerdung. Eine anschauliche Darstellung der menschlichen Stammesgeschichte und eine kritische Betrachtung ihrer allgemeinen Voraussetzungen. Jena: Verlag von Gustav Fischer.
Naef, A. 1933b. Cephalopoda, pp. 293—310 in Dittler, R., Joos, G., Korschelt, E. Linck, G., Oltmanns, F. and Schaum, K. (editors) Handwörterbuch der Naturwissenschaften, 2nd edition, volume 2. Jena: Verlag von Gustav Fischer.
Naef, A. 1933c. Morphologie der Tierre (Allegmeines und Grundsätzliches), pp. 3—17 in Dittler, R., Joos, G., Korschelt, E. Linck, G., Oltmanns, F. and Schaum, K. (editors) Handwörterbuch der Naturwissenschaften, 2nd edition, volume 7. Jena: Verlag von Gustav Fischer.
Naef, A. 1972a. Cephalopoda. Fauna and Flora of the Bay of Naples (Fauna und Flora des Golfes von Neapel und der Angrenzenden Meers-Abschitte), Monograph 35, Part I, [Vol. I], Fascicle I. Smithsonian Institute Libraries, Washington.
Naef, A. 1972b. Cephalopoda (systematics). Fauna and Flora of the Bay of Naples (Fauna e Flora del Golfo di Napoli), Monograph 35, Part I, [Vol. I], Fascicle II. Washington, Smithsonian Institute Libraries.
Naef, A. 2000. Cephalopoda. Embryology. Fauna and Flora of the Bay of Naples [Fauna und Flora des Golfes von Naepel]. Monograph 35. Part I, Vol. II [Final part of the Monograph No. 35], pp. 3-461. Washington, Smithsonian.