Monday, November 14, 2022

Skull Retrodeformation Notes

 1. Use of warp on back left crest, not affecting nasal passages. 5 warp points to uncave-in / fix some caved in places

2. Use of elastic deformation brush in sculpting mode to straight out crest -- again, in the places where there are not nasal passages. 

3. Testing to see if I can group together skull and nasal then use elastic deformation rather than blending to straighten out the nasals, which are currently a bit twisted weirdly towards the left. 

4. My plan is to expand nasals & skull to at least as wide as the CMN skull.

Sunday, November 13, 2022

Links for reference, blender

 https://www.embodi3d.com/blogs/entry/129-3d-printing-of-bones-from-ct-scans-a-tutorial-on-quickly-correcting-extensive-mesh-errors-using-blender-and-meshmixer/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5098973/

https://github.com/evaherbst/MyoGenerator

https://www.researchgate.net/publication/271192743_The_walking_dead_Blender_as_a_tool_for_paleontologists_with_a_case_study_on_extinct_arachnids

https://www.frontiersin.org/articles/10.3389/feart.2022.833379/full

https://pubmed.ncbi.nlm.nih.gov/36039284/

https://twitter.com/Tom_Dudgeon/status/1509947978211020811/photo/2

Wednesday, November 2, 2022

Acoustic simulation work log

I started with trying to use i-Simpa to do acoustical analysis on hadrosaur nasal passages. I'm using Windows bootcamp on my work laptop to run it. Windows is the devil, but I took a stab -- and determined that trying to built it in arm64 OSX 10.12 is an exponentially worse time sink that I do not actually need to do. 

First, I have to export the model in 3ds format. That means I have to simplify it to MAX_INT vertices. It's a specific number, but hey, it's the 16-bit int max, so that's what I remember. 

I'm simplifying in Meshlab.... 

A second later, I realize it does open stl. Dur. However, simplified vertices are probably better for this kind of thing.

Okay! I ran into some early problems, and although there are some comments on the webpage it can be used for any 3D object, i-Simpa is designed for rooms only after. And I stumbled on this recommendation:
https://acousto.sourceforge.net/

It works on OS X. 

OKAY! I'm going to do that. 
++had to replace the config.guess & config.sub
++mired in build errors with BLAS, SCALAPACK, etc. 
++tried to install via dockerfile 
++dockerfile starts with the same config.guess & config.sub errors
++realized last update was 2017. sigh......... free software... you know. anyways, of course everything is hosed.
++running 6yo docker image. I can test v.1.6 out at least. maybe tomorrow tho, feeling fed up

And then I found this: 
https://computational-acoustics.gitlab.io/website/posts/0-modelling-acoustics-with-open-source-software/

http://www.openpstd.org/index.html
A plug-in for blender

http://www.k-wave.org/
plug-in for matlab -- apparently can be used with "tissue-related media"
it may work in octave:
http://www.k-wave.org/forum/forum/octave
their list of alternative acoustics software:
http://www.k-wave.org/acousticsoftware.php

______

1. Once you use the same OS and UI for 20 years others are almost always clumsy and horrible no matter what. I do every now and then have to do Windows stuff and code in Windows and get my software working on Windows. BUT IMO, objectively horrible things about Windows are the registry tree, writing Windows installers, and how it handles hardware drivers. Also, some of the old Windows API was really needlessly convoluted. I haven't seen it in 10-15 years, so I expect that has improved with changing software standards, etc. And to be very, writing installers or making anything work across multiple machines and OS's is something I find super tedious, error-ridden, and annoying across the board. 

Friday, October 28, 2022

Paranasal air sinuses of predatory and armored dinosaurs, pt. 2

Witmer & Ridgely paper: 

Witmer, L. M., & Ridgely, R. C. (2008). The paranasal air sinuses of predatory and armored dinosaurs (Archosauria: Theropoda and Ankylosauria) and their contribution to cephalic structure. The Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology: Advances in Integrative Anatomy and Evolutionary Biology, 291(11), 1362-1388.

Notes:

++ Nasal passages of the Majongasaurus and the T. Rex more closely resemble those of an ostrich than an alligator. "Anteorbital cavity is open laterally" and thus only covered by skin. Majongasaurus and T. Rex both had very extensive nasal sinuses that were pneumatized, even inflating bone. Eg. in T. Rex the palatine bone was inflated. T. Rex had larger nasal sinuses than Majongasaurus.

Terms: 

strut -- a structure to resist (generally) longitudinal compression. The face consists of many bones that act as struts. (wikipedia)

septa - walls, dividing a cavity or structure into smaller ones. (wikipedia)

lobular -a lobe is a clear anatomical division or extension[1] of an organ (as seen for example in the brain, lung, liver, or kidney) that can be determined without the use of a microscope at the gross anatomy level. (again, wikipedia)

ramus (plural rami) A small spray or twig. (biology) A branching, as of nerves or blood vessels. (wikipedia)

evaginate -(with reference to a tubular or pouch-shaped organ or structure) turn or be turned inside out. "the sacs evaginate and come to lie externally" from Oxford Languages

Palatine bone on a human:




Passage about nasal resonation in humans:
Re: singing in "the mask". Yes, I remember this phrase from my years being classically trained in voice. It is interesting how I can relate my personal experience to dinosaur research -- which -- I suppose is the point of this work (Rawr!, Dinosaur Choir) -- in a sense. 

Thursday, October 27, 2022

Open-source acoustical analysis tools

i-Simpa
https://i-simpa.univ-gustave-eiffel.fr/

PachydermAcoustic
https://github.com/PachydermAcoustic

 

Paranasal air sinuses of predatory and armored dinosaurs, pt. 1

Witmer, L. M., & Ridgely, R. C. (2008). The paranasal air sinuses of predatory and armored dinosaurs (Archosauria: Theropoda and Ankylosauria) and their contribution to cephalic structure. The Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology: Advances in Integrative Anatomy and Evolutionary Biology, 291(11), 1362-1388.

Summary: Examines and compares archosaur nasal passages and sinuses of extinct and extant archosaurs. Focuses on 2 predatory theropods and 2 ankylosaurs, using the living taxa (alligator, ostrich, etc.) to infer soft tissues and compare.

Notes: 

++Used Amira software for segmentation

++In alligators, the antorbital fenestra are lost and their sinuses are enclosed with bone -- like mammals. Compares the antorbital sinus with the mammalian maxillary sinus. Nasal airway is long bc of their second palate.

++This antorbital sinus is the only paranasal sinus shared across Archosauria.  Ostriches, the other living taxa compared, also has one similar to a crocodile. Suborbital sinus is the largest in ostriches.

Terms: 

An ostium (plural ostia) in anatomy is a small opening or orifice. (wikipedia)

Abelisaurids - theropod ceratosaurian dinosaurs, mostly found in the Cretaceous. eg. Carnotaurus. note: Smaller arms than t. rex.

Wednesday, October 19, 2022

Vocalization References

Riede T, Tokuda IT, Farmer CG. Subglottal pressure and fundamental frequency control in contact calls of juvenile Alligator mississippiensis. J Exp Biol. 2011;214:3082–
3095. Accessed from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160820.

Riede, T., Li, Z., Tokuda, I. T., & Farmer, C. G. (2015). Functional morphology of the Alligator mississippiensis larynx with implications for vocal production. The Journal of Experimental Biology, 218(7), 991-998.

Li Z, Clarke JA. New insight into the anatomy of the hyolingual apparatus of Alligator mississippiensis and implications for reconstructing feeding in extinct archosaurs. J Anat. 2015 Jul;227(1):45-61. doi: 10.1111/joa.12320. Epub 2015 May 28. PMID: 26018316; PMCID: PMC4475358.

Robert V. Hill, Michael D. D'Emic, G. S. Bever, Mark A. Norell, A complex hyobranchial apparatus in a Cretaceous dinosaur and the antiquity of avian paraglossalia, Zoological Journal of the Linnean Society, Volume 175, Issue 4, 1 December 2015, Pages 892–909, https://doi.org/10.1111/zoj.12293

Note: https://www.isca-speech.org/archive_v0/Interspeech_2018/pdfs/1080.pdf


Thursday, September 22, 2022

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

Wednesday, September 21, 2022

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/


Tuesday, September 20, 2022

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


Wednesday, September 14, 2022

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


Monday, September 12, 2022

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.

Wednesday, September 7, 2022

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. 

Tuesday, September 6, 2022

Hadrosaur paper notes

Sternberg, C. M. (1964). Function of the elongated narial tubes in the hooded hadrosaurs. Journal of Paleontology38(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


Tuesday, August 30, 2022

Links relating to current research - Participatory Music summary, physically modeling a syrinx, etc.

Helpful summary of Thomas Turino's research:

http://www.ethanhein.com/wp/2014/participatory-music-vs-presentational-music/

Quote:

America suffers from its lack of participatory music

I have a hypothesis that the lack of participatory music in daily American life is a major obstacle to our well-being. Most humans in world history regard social music as a basic emotional vitamin, and our lack of it shows in our collective unhappiness, as clearly as malnutrition shows in stunted bone growth. Children have participatory music opportunities, at home, on the playground, at school, in church and at camp. But as an adult, you really have to make an effort to seek out music-making opportunities. One of the biggest pleasures of having a young kid is all the participatory music-making you do with them.

Yes.

But also, reading it, I think about this research anew in terms of Argentine tango and its social context. 

Turino generally presents dancing as part of participatory music, and I agree. However, reading through the bullet points of the qualities of participatory music, I must look at some of them, and think:

Oh, this doesn't really describe tango music. Oh, parts of this doesn't really describe tango dance even. I'm thinking about this now, although I have read Turino's book for many years.

The entry barriers to Argentine tango can be high. I know people who took two years of lessons before dancing socially. I personally took almost a year of lessons before even going to a practica. When I was at ASU, this wasn't the case, though. New people (students) would often flock to the practicas and the leadership at the club was welcoming and any experienced dancer was charged with being kind and dancing with as many newcomers as possible.

I can't say whether ASU Tango Club was the norm or the exception, but I actually tend to think it's an exception.

But let's look at a few inconsistencies if I am looking at tango through a participatory music lens:

Beginnings/endings are feathered:
Nope. In fact, my only early strength as a dancer was my musical training because the cadences would always hit me in the face whilst my beginning partners kept obliviously dancing through phrase endings and were sometimes startled at the ends of songs. However, if you grow up listening to it or classical music, you know. 

The form of the music is open, cyclical and very repetitive:
Hmmm, more repetitive than Western Art Music but less repetitive than a lot of popular music and contradance music.

There might be a lot of improvisation and looseness, but it all takes place within predictable structures:
Yes, at least the dance. There is something like that in the music, but the music is definitely more presentational. 

Textures and timbres are dense, with loose (“wide”) tuning and timing:
Hmmm, maybe less so on this, but the timing is looser in tango in very characteristic ways, eg. rallentando at cadences. One of the complaints people have about dancing to electro-tango is the rigid timing (and the repetition).

The music is game-like, though usually without “winners” and “losers.”:
Yes, very much so - at least for the dancing. 

It’s made by musicians of widely varying skill. Most participants are “amateurs,” not “real” musicians by American standards. There’s a low floor for core participation, like shaking a shaker steadily, and a high ceiling for elaboration, like virtuoso lead percussion:
Argentine tango dancers are generally not professional dancers, yes, but the bar is higher. There's an emphasis on competence and virtuosity that (IMO) really outstrips other dances in terms of the social scene. We say the basic step is walking, but um, you have to relearn walking a LOT over many years.

Overall Argentine tango is I think, participatory music in terms of movement and dancers, but not in terms of the sound/musicians. Certainly during 20s-40s in Buenos Aires you needed to dance to properly socialize. It's not like salsa or swing, tho, where the entry barrier is relatively low. 

I see why it is a subculture, though. Certainly contemporary tango emphasizes competency and an explicit set of social norms and etiquette that many dancers will respond negatively if broken. Some city scenes are not welcome to beginners and newcomers (some are). My love for tango music meant that I was willing to be initiated and spend multiple years developing a competency and a familiarity, but it's not like contradance, where you can just go and dance and be a part of everything from the start. At least, that wasn't my experience.

Syrinx modeling:

Classic Smyth (& Smith & Abel):

https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.128.6431&rep=rep1&type=pdf

https://www.dafx.de/papers/DAFX02_Smyth_Smith_flute-like_sounds.pdf

http://www.dafx.de/paper-archive/2004/P_095.PDF

https://asa.scitation.org/doi/abs/10.1121/1.4781002

https://www.researchgate.net/profile/Tamara-Smyth/publication/247868491_THE_ESTIMATION_OF_BIRDSONG_CONTROL_PARAMETERS_USING_MAXIMUM_LIKELIHOOD_AND_MINIMUM_ACTION/links/55159cc50cf2d70ee270e85f/THE-ESTIMATION-OF-BIRDSONG-CONTROL-PARAMETERS-USING-MAXIMUM-LIKELIHOOD-AND-MINIMUM-ACTION.pdf

The NIME:

https://arxiv.org/pdf/2010.03265.pdf

More recent, biologically (as in discipline) motivated research: 

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.84.051909

https://asa.scitation.org/doi/10.1121/1.395910 (not recent, but cited)

https://asa.scitation.org/doi/10.1121/1.395910

(some unrelated stuff for my purposes, but has citations to more related things)
https://www.sciencedirect.com/science/article/pii/S0960982221007338?casa_token=D8ZH7KdLEfoAAAAA:cfhtlgkjIvz__Y7wItfSIXqev-NGZPdwxLi7CxD1kOLD_0kp3rSEQsBBDmz-fOcMlaa8-ctOdhg#!

(newer, less biologically motivated -- audio engineering not bio)
http://www.eecs.qmul.ac.uk/~josh/documents/2019/20578.pdf