title graphic

DEVO@CU is an attempt to build a coherent introduction to the key ideas, observations & model systems used to study embryonic development. It is built on the biofundamentalist perspective (link)

Thoughts on course organization are outlined on the bioliteracy.blog:



Syllabus - there may weill be changes before the course starts and along the way

Date / Topic   to be completed before class - jump to current week


Tues, 14 Jan. 2020

What is the course
about, how does it
work & what do we expect from you?

class 1 slides  


+ intro to beSocratic & nota bene & how to read a paper (communally)

nothing required before the first day!

background reading for the class:
On teaching developmental biology in the 21st centrury - Klymkowsky (blog)

useful reference works: Nature: Milestones in developmental biology


Thurs. 16 Jan.

Genes, experimental methods & outcomes

class 2 slides 


beSocratic BEORE class: #1 What is a gene next class

read/review BEFORE class:
Genes – way weirder than you thought
  - Klymkowsky (blog)
The evolving definition of the term “gene” - Portin & Wilkins 2017

totally optional (supporting):
Your Cancer Targets may not be real - Lowe. 2019
Off-target toxicity is a common mechanism of action of cancer durgs undergoing clinical trials - Lin et al. 2019
Biological plasticity rescues target activity in CRISPR knock outs - Smits et al 2019
watch/review: Cre-Lox recombinase
CRISPR: Gene editing and beyond & RNA interference (RNAi)


Tues  21 Jan.

Decision making
in bacteria:
behaviors, sampling phenotypic space
& non-linear

→ class 3 slides


beSocratic BEORE class: #2. Molecular numbers and half-lives
& #3.Genotypes, phenotypes & noise

read/review BEFORE class:
Molecular machines & the place of physics in the biology curriculum - Klymkowsky (blog)
Stochastic gene expression in a single cell - Elowitz 2002 

totally optional (supporting):
Biology education in the light of single cell/molecule studies - Klymkowsky (blog)
Distinct mods of cell competition shape mammalian tissue morphogenesis - Ellis et al., 2019
Cellular decision making & biological noise – Balazsi et al 2011


Thurs 23 Jan.


→ class 4 slides


beSocratic BEORE class: #4. Community behaviosr & quorum sensing,

read/review BEFORE class:
Aggregative & clonal metazoans – Klymkowsky (blog)
Bacterial quorum-sensing network architectures. - Ng and Bassler 2009

totally optional (supporting):
The social lives of microbes– West et al. 2007
Collective behaviour & swarm intelligence in slime moulds – Read & Latty 2016


Tues,  28 Jan.


→ class 5 slides


beSocratic BEORE class: #5 Clonal behaviors

 read BEFORE class:
The origins of animal multicellularity - Bonner 1998

totally optional (supporting):
The evolution of metazoan axial properties - Martindale. 2005
The origin of animal multicellularity and cell differentiation - Brunet & King 2017


Thurs,  30 Jan.

Cellular polarity
& asymmetry

→ class 6 slides


beSocratic BEORE class:  #6 Emerging cellular polarities

read BEFORE class
Dividing cellular asymmetry - Neumuller & Knoblich. 2009

totally optional (supporting):
Remodeling epithelial cell organization: front-read and apical-basal polarity - Nelson 2009
Front–Rear Polarization by mechanical cues - Ladoux et al 2016
Orienting muscle stem cells - Feige et al. 2018
The in(side) & outs(ide) of asymmetric stem cell division. - Chen et al 2016


Tues, 4 Feb.

& left-right

→ class 7 slides


beSocratic BEORE class: #7 Molecular and cellular left-right asymmetry

read BEFORE class:
Molecular to organismal chirality ... conserved myosin 1D - Lebreton et al., 2018

totally optional (supporting):
Daughter 3T3 cells: Are they mirror images of each other? - Albrecht-Buehler 1977
Cellular chirality regulates left-right symmetry breaking during cardiac looping. - Ray et al., 2018.


Thurs, 6 Feb.

Morphogensis &
axes: signaling
gradients &
decision making

→ class 8 slides


beSocratic BEORE class: #8 Gradients and threshold effects

read BEFORE class
A mechanism for the sharp transition of morphogen gradient interpretation -Saka & Smith 2017

totally optional (supporting):
Morphogen rules: design principles of gradient-mediated patterning. - Briscoe & Small. 2015
Morphogen transport  - Muller et al 2013


Weeek 5:
Tuesday, 11 Feb.

Establishing (AP)
axes (Hox)

→ class 9 slides


beSocratic BEORE class: #9 Establishing axis & tissue polarity

read before class:
Hox genes, homeosis and the evolution of segment identify: no need for hopeless monsters - Akam 1998

totally optional (supporting):
On the evolution of bilaterality - Genikhovish & Technau. 2017
The rise and fall of Hox gene clusters -Duboule 2007
The enigmatic HOX genes: can we crack their code?  Luo et al 2019
Control of Hox transcription factor concentration and cell-to-cell variability by an auto-regulatory switch - Papadopoulos et al. 2019.


Thursday, 13 Feb



review questions on nota bene


Week 6:
Tuesday, 18 Feb.

  MIDTERM #1  First midterm exam   Answer key from 2019


Thursday, 20 Feb.

Model systems

→class 10 slides


beSocratic BEORE class: #10 Characteristics of model systems

Read before class: 
Mouse models of human disease: an evolutionary perspective - Perlman 2016.

totally optional (supporting):
Model organisms - P. Murphy
Mice fall short as test subjects for some of humans’ deadly ills - McGlinn 2013
Gene losses during human origins - Wang et al 2006
Recent de novo origin of human protein-coding genes - Knowles &McLysaght 2009
Massively parallel dissection of human accelerated regions in human and chimpanzee neural progenitors - Ryu et al 2019
False analogies & logical fallacies in animal models - Sjoberg 2016


Tues,  25 Feb.

Reflecting on the
first midterm
("I know it now")

Learning from
the frog

→class 11 slides


beSocratic BEORE class: #11. Axis formation in Xenopus: change detection systems

read before class
Evidence that fold-change, and not absolute level, of β-catenin dictates Wnt signaling
- Goentoro & Kirscher 2009

totally optional (supporting):
Richard Harland on Xenopus: part 1
Cortical rotation and messenger RNA localization in Xenopus axis formation. - Houston, 2010
Fold-change detection in biological systems. - Adler & Alon 2018


Thurs., 27 Feb.

Completing the frog (emerging cell types)

→class 12 slides


beSocratic BEORE class: #12 Developmental trajectories

read before class
The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution - Briggs et al. 2018 (read summary page)

totally optional (supporting):  
Principle Component Analysis, explained simply - BioTurning
Volcabo plot | Violin plot - Wikipedia


Tue, 3 March

Learning from the fly
& genetic screens

→ class 13 slides


beSocratic BEORE class: #13 Genetic screens in the fly

read on before class
How the dorsal gradient works: insights from postgenome technologies - Hong et al., 2008

totally optional (supporting):
Drosophila as a model organism - Yamaguchi & Yoshida 2018


Thurs, 5 March

finishing the fly

→ class 14


beSocratic BEORE class: #14 Homeotic mutations

read on before class
The Heidelberg screen for pattern mutants of Drosophila: a personal account - Wieschaus & Nusslein-Volhard 2016

totally optional (supporting): watch this space!


Tues, 10 March

Learning from worm: lineages & cell death

→class 15 slides


beSocratic BEORE class: #15 Cell lineage (C. elegans)

read on before class
A transparent sindow into biology: a primer on Caenorhabditis elegans
- Corsi et al 2015

totally optional (supporting):
The natural history of Caenorhabditis elegans
- Felix & Braendle 2010
Cell Death C. elegans development
- Malin & Shaham 2015


Thurs, 12 March


class 16 slides


beSocratic BEORE class: #16 Emerging asymmetric (mouse)

read on before class: :
Cell fate decisions and axis determination in the early mouse embryo
- Takaoka & Hamada 2012

totally optional (supporting):
watch : mouse embryo imaging


WEEK 10:
Tues, 17 March

+ Exam Review

review questions are also on nota bene


Thurs, 19 March

  MIDTERM #2 Second midterm exam  

Spring Break    


WEEK 11:
Tues,  31 March

Gastrulation & Neurulation

class 17 slides


beSocratic BEORE class: #17 Morphogenic movements (gastrulation / neurulation)

watch through [link] to ~12:20
Time-lapse through neurulation
Richard Harland on gastrulation:

Mouse :
Animation: Second Week Of  Development
Animation: Gastrulation | Neurulation

totally optional (supporting): watch this space


Thurs, 2 April

network, clocks
& wavefronts

class 18 slides


beSocratic BEORE class: #18 Somites clocks and wavefronts

read / review before class
The mechanism of somite formation in mice– Saga 2012.

totally optional (supporting):
Patterning embryos with oscillations: structure, function anddynamics of the vertebrate segmentation clock - Oates et al 2012


WEEK 12:
Tues,  7 April

Spinal cord &
neural tube

class 19 slide


beSocratic BEORE class: #19 A/P and D/V Neural patterning

read / review before class
Development-on-chip: in vitro neural tube patterning with a microfluidic device - Demers et al 2016

totally optional (supporting):
Wnt/β-Catenin Signaling during Early Vertebrate Neural Development - Brafman & Willert 2017
Establishing neuronal diversity in the spinal cord - Sagner & Briscoe 2019


Thurs, 9 April

Neural crest

class 20 slides


beSocratic BEORE class: #20 Neural Crest induction & epithelial-mesenchymal transition

read / review before class
Identification of a rudimentary neural crest in a non-vertebrate chordate - Abitua et al 2012

totally optional (supporting):
Ancient evolutionary origin of vertebrate enteric neurons from trunk-derived neural crest - Green et al 2017
The neural crest migrating into the twenty-first century. Bronner & Simoes-Costa. 2016


WEEK 13:
Tues,  14 April

Limb formation

class 21 slides


beSocratic BEORE class: #21. Pattering the vertebrate limb

read / review before class
On the Formation of Digits and Jointsduring Limb Development
- Hiscock et al 2017

totally optional (supporting):
 Specialized filopodia direct long-range transport of SHH during vertebrate tissue patterning - Sanders et al 2013


Thurs, 16 April

effects on

class 22 slides


beSocratic BEORE class: #22 Environmental and viral influences

read / review before class
 In vitro neural tube patterning with a microfluidic device
- Demers et al 2016

totally optional (supporting):
Impact of fetal alcohol syndrome on body systems: a systemtic review - Caputo et al, 2016
Fetal and neonatal abnormalities due to congenital rubella syndrome: a review of literature
- Yazigil et al 2017


WEEK 14:
Tues, 21 April

Stem (ES) &
iPSC cells

→class 23 slides


beSocratic BEORE class: #23. Cellular reprogramming

read / review before class
 Impact of fetal alcohol syndrowm on body systems: a systemtic review
- Demers et al 2016

totally optional (supporting):
 Comparing ESC & iPSC - Based models for human genetic disorders - Halevy & Urbach 2014
Embryoids, organoids and gastruloids: new approaches to understanding embryogenesis - Simunovic & Brivanlou 2017


Thurs, 23 April

human / primate

class 24 slides


beSocratic BEORE class: #24.Building tissues de novo

read / review before class
 Using brain organoids to understand Zika virus-induced microcephaly
- Qian et al 2017

totally optional (supporting):
Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution - Pollan et al 2019
Cell types of the human retina and its organoids at single-cell resolution: developmental convergence, transcriptomic identity, and disease map - Cowan et al 2019


WEEK 15:
Tues,  28 April

Gene editing
in embryos

class 25 slides


beSocratic BEORE class: #25.In vivo gene editing

Gene editing is here. It’s an enormous threat.
- Thiessen 2018

read on NB before class
What are the Ethical Concerns of Genome Editing?

totally optional (supporting):


Thurs, 30 April

class 26 slides


REVIEW for third midterm & comprehensive exam

Course review questions - part 1
+ Course review questions - part 2




last year's answer key

molecular buff  

The original version of DEVO@CU by M.W. Klymkowsky/virtuallaboratory/beSocratic, llc.| part of the the biofundamentals cooperative
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.  2019-2020