Computer and parts for computational dino larynx, Prototype 1 notes

My goal is to get some hardware up and running asap for a computational dino larynx. I did let some pure coding/dsp research sort of bottleneck me up on that end, but no more. 

My prototype 1 idea is just this: 
Raspberry Pi 4
Contact mic + usb adaptor to very easily go into raspberry pi as a breath sensor. I've used it as a breath sensor in another project, so it'll be at least good for 1st prototype.
Speakers, TBD -- looking for super cheap ideas for prototype 1, for now, I have headphones, but I want to get this system in a shape PRONTO so that I could install it a skull, so I can start designing and printing skulls. Main problem I see is lower end of the frequency on relatively small speakers -- but there are relatively headphones with good low-end now so I'm guessing there are options...

If I need a better anything, I'll replace as needed. And/or if I get grant money, I'll replace with better. 

I'm strongly leaning towards just using C++ DSP stuff to power my models & probably with Perry Cook's STK to power filters, etc. Or perhaps the related library LEAF. Leaning towards STK, tho, since bc Raspberry Pi runs linux and alsa now is bundled with linux, then it should be compatible. I couldn't find anything specific using STK with raspberry pi, but I think it should relatively painlessly. Also (in what I think is a minority opinion) I prefer coding in C++. It also looks like STK was last updated 7mo. ago or so, which is not terrible. 

I did look at Sid Fel's Artisynth for larynx modeling -- and it is super intriguing. I am definitely interested in it for a later prototype down the road but ultimately decided against it for the time being because the software is married to intel processors, limiting my hardware options if I were to use it (eg, no RPI). 

Anyhow, I am feeling comfortable with my direction finally, since everything is relatively modular and can be upgraded/replaced (incl. code/software) relatively easily.

Also, this looks like a cool library:
https://hal.archives-ouvertes.fr/hal-02270792/document

And just a bookmark, schematic for wind instrument from ccrma:
https://ccrma.stanford.edu/~jos/asahb04/Wind_Instruments.html

Dino Papers, Hopson (1975), Pt. 2 & Raspberry Pi dsp link

Hopson, J. A. (1975). The evolution of cranial display structures in hadrosaurian dinosaurs. Paleobiology, 1(1), 21-43.

Notes: He discusses Hadrosaurinae further, which is less useful for my research. However, some interesting ideas. One of them is that they (the Hadrosaurinae that are not kitosaurs) had soft tissue crests (there is more fossil evidence for this now) and also that their diverticula could inflate these via nasal passages for a visual display structure -- perhaps also achieving sound resonation functionality a la the elephant seal. The narial depression seen in these dinosaurs would seem to enable that as he agrees with  Versulys (1936) that the area would be occupied by nasal capsules, their glands, and be ar-filled.

With the mention of the elephant seal, I did do a side excursion of course to look and hear elephant seals:
https://www.youtube.com/watch?v=FpIf6mPZJGA
https://www.pbs.org/newshour/science/elephant-seals-recognize-vocal-rhythms-avoid-bullies

The paper ends with the discussion about how each of the different hadrosaur groups and subgroups may have evolved their differing crests and nasal passages, including speculations on form and function.

And now for computer music interlude, which will eventually tie-in -- some research on raspberry pi:

From Reddit:
https://www.reddit.com/r/diyaudio/comments/ncdmrs/raspberry_pi_for_dsp/

Dino papers: Hopson, 1975, Evolution of Cranial Display Pt. 1

Hopson, J. A. (1975). The evolution of cranial display structures in hadrosaurian dinosaurs. Paleobiology, 1(1), 21-43.

Notes/Summary: This paper was referenced by a few of the Weishampel, so feels like catch-up reading. 

Hopson introduces the idea that the head crests of hadrosaurs were for sexual display -- visual and with the hadrosaur with hollow crests -- audio as well. Crest variations were species and gender-specific and tended to increase (via evolution) with time. Crests varied externally and internally independently of one another and also hadrosaurs had well-developed eyes and ears.  He writes that the hadrosaurs developed diverticula to draw attention to a horn which was used aggressively in mating (he hypothesizes) and then for sexual display (visually) the hollow-crested dinosaurs evolved bone to cover it for acoustic resonation. (all from abstract)

He classifies hadrosaurs into 2 subfamilies (with hollow crests - lambeosaurinae) and without (hadrosaurinae), but in the hadrosaurinae creates 3 subgroups -- kritosaurs, edmontosaurs, saurolophines -- all with non-hollow crests or no bony crests. He believes the ancestral hadrosaurian condition is approximated by kritosaurs -- whilst edmontosaurs are an isolate -- he thinks the deeply excavated narial passages set them apart and all other hadrosaurs have elevated nasal bones in different forms. (including, I assume those that appear earlier in the fossil record).

new term break:

epithelium - The epithelium is a type of body tissue that forms the covering on all internal and external surfaces of your body, lines body cavities and hollow organs and is the major tissue in glands.
https://my.clevelandclinic.org/health/articles/22062-epithelium#:~:text=What%20is%20the%20epithelium%3F,the%20major%20tissue%20in%20glands

In addition to the main olfactory epithelium, the septal organ of Masera (SOM) is another epithelium containing chemosensory neurons. It is located bilaterally on the nasal septum near the entrance of the nasopharynx and is completely encircled by respiratory epithelium (Figure 1). This island of olfactory sensory neurons projects axons to the MOB and targets a subset of glomeruli located in the posterior ventromedial bulb. 
https://www.sciencedirect.com/topics/neuroscience/olfactory-epithelium

**This refers to human olfactory epithelium but helps explicate the term in general.

end.

Questions Hopson poses about previous nasal crest function hypotheses (for -- underwater breathing, olfactory, display and combat organs)
1. Why does selection for above functions (mainly underwater breathing & olfactory) resulted in such diversity of shape among lambeosaurines?

2.  What is the function of the solid crests of the saurolophines?

And relatedly he also asks -- why did lambeosaurines evolve such a complicated way of doing these things that other hadrosaurs presumedly would have also done? In possibly different ways?

Now he argues for social signaling as a function of all crests in hadrosaurs (also after he wrote this note that they found fleshy crests.....). Specifically, he mentioned courtship, mating fights, and sexual selection.  Kritosaurs could have used their crests and humps and horns for combat.

PAUSE pg. 37

Hadrosaur papers #4: More Weishampel

Weishampel, D. B. (1997). Dinosaurian cacophony. Bioscience, 47(3), 150-159.

Notes and terms: 

extant phylogenetic bracketing - first introduced by Witmer in 1995, comparing extinct taxon to nearest living relatives

levels of interference - confidence levels 

pleurokinesis - the hadrosaurid way of chewing

foramen - an opening in a bone for the passage of blood vessels, nerves, muscles, and similar entities (from Wikipedia, in fact)

This paper says that ostriches, emus, and rheas appear to lack syringes, but a quick google search suggests that they do. Perhaps they are different from other birds and thus, weren't recognized. I should do further research.

Because both birds (where it does not serve a vocal function) and crocodiles have larynges, by extant phylogenetic bracketing, we can assume that hadrosaurids also had one. Additionally, the primitive condition for the archosauria is that the larynx is not vocalizing -- because all relatives who split off earlier (out-group comparison) have non-vocalizing larynges. (Note: this is a similar path of logic to the Senter (2008) paper)

ahistorical functional morphology - based on models used to simulate extinct organ function -- from engineering, biology, other relevant fields

new equation for the lateral diverticula (closed at their ends) - 

f = (2n-1)(v/4L)

n - harmonic #
L - tube length

The small diameter of the tube of the parasaurolophus would lend itself to lower frequency resonances. The long length the passageway also favors lower pitches.

lagena - archosaur analogue to cochlea in mammals

hadrosaurid hearing apparatus is consistent with both birds and reptiles

This paper was also interesting in how it approaches the making of inferences and hypothesis and how to consider different kinds of evidence for and against a conjecture about an extinct organism in a more objective way -- that is, when phylogenetic evidence is contra to the functional morphological evidence as in the case with hadrosaurid vocalization. 

A primate excursion - wandering - of research from looking at citations from the last Weishampel paper:

Koda, H., Nishimura, T., Tokuda, I. T., Oyakawa, C., Nihonmatsu, T., & Masataka, N. (2012). Soprano singing in gibbons. American Journal of Physical Anthropology, 149(3), 347-355.

and the youtube video:

https://www.youtube.com/watch?v=Qm0p2ZoABfo

(Weishampel paper does not mention gibbons, but howler monkeys, but somehow I ran into gibbon calls, which are truly awesome and I love them)

Ahem, back to more related research, via earlier Weishampel paper of the last post, the resonating structure of the howler monkeys is hypothesized to be their hyoid bone, which, to be fair, is crazy:

Image from: https://evolutionliteracy.com/2015/10/23/evoliteracy-news-10-23-2015/

For comparison: 

The hyoid bones of other primates. Image from: https://www.researchgate.net/figure/Different-hyoid-bone-models-from-different-primates-C-Bone-Clones-wwwboneclonescom_fig10_236608209

Fitzpatrick, J. L., & Lüpold, S. (2015). Evolution: big bawls, small balls. Current Biology, 25(22), R1084-R1086.

Apparently, the size of hyoid tends to be inverse to the size of the ball sac. Um, okay!

And...the listen to the monkey:

https://www.youtube.com/watch?v=PYar0dkZ6v8

Hadrosaur Papers, Notes #3

Weishampel, D. B. (1981). Acoustic analyses of potential vocalization in lambeosaurine dinosaurs (Reptilia: Ornithischia). Paleobiology, 7(2), 252-261.

Notes/Summary: This covers the Wiman paper in the context section. Of interest is the comparison between parasaurolophus skulls and the krumlur and as well as the trumpeter and whistling swans. Weishampel speculates a vocal organ between the phranx and the lungs would make the nasal passages work well as a resonator. This is in a similar place to trumpeter swan.

L = n(λ/2)

n = resonance mode
L - tube length

f = n(v/2L)

The soft tissues in Corythosaurus and Lambeosaurus likely changed the contours of the nasal passages more than Parasaurolophus, and thus, the sounds.

Other animals have resonating chambers in their skull similar to the lateral diverticula of Corythosaurus and Lambeosaurus such as some crocodiles, dolphins, microchiropteran bats, and howler monkeys.

He also addressed the ear and hearing ranges, which was covered in more depth in the more recent Evans & Witmer paper.

Hadrosaur papers (cont.)

Weishampel, D. B. (1981). The nasal cavity of lambeosaurine hadrosaurids (Reptilia: Ornithischia): comparative anatomy and homologies. Journal of Paleontology, 1046-1057.

Notes/Summary (cont): Juveniles of Corythosaurus casuarius and the lambeosaurus do not have lateral diverticula -- so that is developed later (it is smaller in the subadult Corythosaurus that I have worked with in the past). With both these species, as the nasal cavity develops, so does the form (eg. developing the LD - the common median chamber moves back caudodorsally (towards the tail, on top) to sit on top of the cranium (brain case) ).

More terms: 

fontanellae - soft spots on an infant's head where the bony plates that make up the skull have not yet come together. 

Hadrosaur paper notes

Sternberg, C. M. (1964). Function of the elongated narial tubes in the hooded hadrosaurs. Journal of Paleontology, 38(5), 1003-1004.

My summary: Early paper. Sternum describes the head crest anatomy, particularly in regards to where the olfactory organ is. The tubes are an extension of the narial tubes in the premaxillae (nasal passages in the upper part of the head/jaw).  Because of the climate, he believes that thermoregulation was not necessary for hadrosaurs. He also notes the position of the tubes vis a vis the nasal capsule/organ does not seem to facilitate better access to incoming air, thus for that and other reasons, he concludes tubes were for underwater feeding. Note: This is an out of date hypothesis because we do not think that hadrosaurs lived or fed underwater.

Wiman, C. 1931. Parasaurolophus tubicen n. sp. aus der Kreide in New Mexico. Nova Acta Regiae Societatis Scientiarum Upsliensis, Ser. IV 7:1–11.

Note: This paper was entirely in German, so I might need to track down a translation. Summary, notes, forthcoming. From brief summaries in other papers, it appears he is arguing that the head crest resulted from / was used for sociosexual reasons/selection.

Weishampel, D. B. (1981). The nasal cavity of lambeosaurine hadrosaurids (Reptilia: Ornithischia): comparative anatomy and homologies. Journal of Paleontology, 1046-1057.

My summary/notes: Description of anatomy. I found this S-loop from the above reference figure very helpful:

Particularly as other papers reference this S-loop.

This is a very technical description of anatomy. I've put some terms down for my re-reading and edification. 

Reading paused on p. 1050. 

Terms: 

soft palate - velum

premaxilla - upper jaw, part of head

rostral - towards nose/head

caudal - towards tail

caudodorsal - near the end of the tail

ventral - underside, belly

dorsal - upperside, back

choana -An opening at the back of the nasal passage 

subequal - almost but not exactly equal

diverticulum - an outpouching of a hollow (or a fluid-filled) structure in the body.

nares, narial - nostril, nasal