The document summarizes key points from Chapter 5 of Andreas Wagner's book on the origins of evolutionary innovations. The chapter examines how metabolic networks, regulatory circuits, and protein/RNA folds evolve under a common principle. It finds that there are typically many more possible genotypes than phenotypes for biological systems. Genotype networks, where genotypes differ by single mutations but share a phenotype, tend to be large, interconnected, and span a broad region of genotype space. This allows populations to explore the genotype space and facilitates the discovery of innovations through neutral drift.
Thesis defence of Dall'Olio Giovanni Marco. Applications of network theory to...Giovanni Marco Dall'Olio
This is the presentation of my PhD thesis defence. It describes two applications of network theory to improve the methods to understand genetic adaptation in the human genome.
Thesis defence of Dall'Olio Giovanni Marco. Applications of network theory to...Giovanni Marco Dall'Olio
This is the presentation of my PhD thesis defence. It describes two applications of network theory to improve the methods to understand genetic adaptation in the human genome.
Synonymous mutations as drivers in human cancer genomes.Fran Supek
Synonymous mutations change the sequence of a gene without directly altering the sequence of the encoded protein. Here, we present evidence that these "silent" mutations frequently contribute to human cancer. Selection on synonymous mutations in oncogenes is cancer-type specific, and although the functional consequences of cancer-associated synonymous mutations may be diverse, they recurrently alter exonic motifs that regulate splicing and are associated with changes in oncogene splicing in tumors. The p53 tumor suppressor (TP53) also has recurrent synonymous mutations, but, in contrast to those in oncogenes, these are adjacent to splice sites and inactivate them. We estimate that between one in two and one in five silent mutations in oncogenes have been selected, equating to ~6%- 8% of all selected single-nucleotide changes in these genes. In addition, our analyses suggest that dosage-sensitive oncogenes have selected mutations in their 3' UTRs.
Aim1: To study the method of genome identification through ENSEMBL browser.
Aim2: To study the method of genome identification through VISTA.
Aim3: To study the method of genome identification through UCSC Genome Browser.
Aim4: To study the method of genome and amino acid sequences through UCSC Genome Browser.
Comparative genome analysis requires high quality annotations of all genomic elements. Today’s sequencing projects face numerous challenges including lower coverage, more frequent assembly errors, and the lack of closely related species with well-annotated genomes. Precise elucidation of the many different biological features encoded in any genome requires careful examination and review. We need genome annotation editing tools to modify and refine the location and structure of the genome elements that predictive algorithms cannot yet resolve automatically. During the manual annotation process, curators identify elements that best represent the underlying biology and eliminate elements that reflect systemic errors of automated analyses.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, analogous to Google Docs, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Researchers from nearly one hundred institutions worldwide are currently using Apollo for distributed curation efforts in over sixty genome projects across the tree of life: from plants to arthropods, to fungi, to species of fish and other vertebrates including human, cattle (bovine), and dog.
Synonymous mutations as drivers in human cancer genomes.Fran Supek
Synonymous mutations change the sequence of a gene without directly altering the sequence of the encoded protein. Here, we present evidence that these "silent" mutations frequently contribute to human cancer. Selection on synonymous mutations in oncogenes is cancer-type specific, and although the functional consequences of cancer-associated synonymous mutations may be diverse, they recurrently alter exonic motifs that regulate splicing and are associated with changes in oncogene splicing in tumors. The p53 tumor suppressor (TP53) also has recurrent synonymous mutations, but, in contrast to those in oncogenes, these are adjacent to splice sites and inactivate them. We estimate that between one in two and one in five silent mutations in oncogenes have been selected, equating to ~6%- 8% of all selected single-nucleotide changes in these genes. In addition, our analyses suggest that dosage-sensitive oncogenes have selected mutations in their 3' UTRs.
Aim1: To study the method of genome identification through ENSEMBL browser.
Aim2: To study the method of genome identification through VISTA.
Aim3: To study the method of genome identification through UCSC Genome Browser.
Aim4: To study the method of genome and amino acid sequences through UCSC Genome Browser.
Comparative genome analysis requires high quality annotations of all genomic elements. Today’s sequencing projects face numerous challenges including lower coverage, more frequent assembly errors, and the lack of closely related species with well-annotated genomes. Precise elucidation of the many different biological features encoded in any genome requires careful examination and review. We need genome annotation editing tools to modify and refine the location and structure of the genome elements that predictive algorithms cannot yet resolve automatically. During the manual annotation process, curators identify elements that best represent the underlying biology and eliminate elements that reflect systemic errors of automated analyses.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, analogous to Google Docs, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Researchers from nearly one hundred institutions worldwide are currently using Apollo for distributed curation efforts in over sixty genome projects across the tree of life: from plants to arthropods, to fungi, to species of fish and other vertebrates including human, cattle (bovine), and dog.
Nuclear Genomes(Short Answers and questions)Zohaib HUSSAIN
1. What did researchers find when they sequenced the centromeres of Arabidopsis? Why was this finding surprising?
Ans: Before the Arabidopsis sequences were obtained it was thought that these repeat sequences were by far the principal component of centromeric DNA. However, Arabidopsis centromeres also contain multiple copies of genome-wide repeats, along with a few genes, the latter at a density of 7–9 per 100 kb compared with 25 genes per 100 kb for the noncentromeric regions of Arabidopsis chromosomes. The discovery that centromeric DNA contains genes was a big surprise because it was thought that these regions were genetically inactive.
2. What differences in gene distribution and repetitive DNA content are seen when yeast and human chromosomes are compared?
Ans. A typical region of a human chromosome will have few genes (most of which will contain introns), several repeated sequences, and a large amount of nonrepetitive, nongenic DNA. Yeast chromosomes have higher gene densities, with very few genes containing introns, and have few repeated sequences and much less nongenic DNA.
3. The human genome contains about 50,000 fewer genes than was predicted by many researchers. Why were these initial predictions so high?
Ans. These early estimates were high because they were based on the supposition that, in most cases, a single gene specifies a single mRNA and a single protein. According to this model, the number of genes in the human genome should be similar to the number of proteins in human cells, leading to the estimates of 80,000–100,000. The discovery that the number of genes is much lower than this indicates that alternative splicing, the process by which exons from a pre-mRNA are assembled in different combinations so that more than one protein can be coded by a single gene is more prevalent than was originally appreciated.
4. What are the different methods used to catalog genes? What are the advantages or disadvantages of these methods?
Ans. Gene catalogs can be based on the known functions of genes, but such catalogs are incomplete because in most genomes many genes have unknown functions. Gene catalogs that are based on the identities of protein domains coded by genes are more comprehensive as these include many genes whose specific functions are unknown.
5. What is the function of the different genes in the human globin gene families?
Ans. The globins are the blood proteins that combine to make hemoglobin, each molecule of hemoglobin being made up of two a-type and two b-type globins.The a-globin cluster is located on chromosome 16 and the b-cluster on chromosome 11. Both clusters contain genes that are expressed at different developmental stages and each includes at least one pseudogene. Note that expression of the a-type gene x2 begins in the embryo and continues during the fetal stage; there is no fetal-specific a-type globin. The q pseudogene is expressed but its protein product is inactive. None of the other p
This presentation was created by Ioanna Leontiou and it is intended as a creative and flexible tool for students on Biological sciences who focus on the chromosome segregation. It is created to facilitate students performing research projects in our lab (especially during Covid restrictions), but it is suitable for every student who wants to learn more about chromosomes and the molecular mechanism controlling chromosome segregation. The presentation includes a generic overview of the cell division, illustrates the chromosome structure and provides molecular details of the spindle assembly checkpoint, an important pathway that ensures high fedility of chromosome segregation through mitosis. It also includes an introduction to some of the molecular biology techniques used in a yeast lab and incoporates some fluorescent microscopy images/videos. At the end of the presentantion there is a list of open access scientific publications for further reading on the the molecular mechanism of spindle checkpoint and some links of some very interesting sites, which include a range of videos on laboratory molecular biology techniques, research talks and guided papers. The purpose of this presentantion is to create a piece of work that students could return to when needed. Diagramms and illustrations are also encouranged to be used by scientists, science communicators and educators.
This presentation is licensed under a Creative Common Attribution-ShareAlike 4.0 (CC BY-SA 4.0), unless otherwise stated on the specific slide.
Comparative genome analysis requires high quality annotations of all genomic elements. Today’s sequencing projects face numerous challenges including lower coverage, more frequent assembly errors, and the lack of closely related species with well-annotated genomes. Precise elucidation of the many different biological features encoded in any genome requires careful examination and review. We need genome annotation editing tools to modify and refine the location and structure of the genome elements that predictive algorithms cannot yet resolve automatically. During the manual annotation process, curators identify elements that best represent the underlying biology and eliminate elements that reflect systemic errors of automated analyses.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, analogous to Google Docs, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Researchers from nearly one hundred institutions worldwide are currently using Apollo for distributed curation efforts in over sixty genome projects across the tree of life: from plants to arthropods, to fungi, to species of fish and other vertebrates including human, cattle (bovine), and dog.
1. Genomics is the study ofa. The structure and function of m.docxblondellchancy
1. Genomics is the study of:
a. The structure and function of mutations and how they alter genetic traits.
b. Genes and the DNA sequences between genes and how they determine development.
c. The information provided by computer programs which analyzes mRNA.
d. The human genome as compared to other vertebrate genomes.
2. Microarrays are a very useful tool in genomics because they:
a. Help scientists examine intergenetic DNA by separating it from genes.
b. Provide a unique promoter region for polymerase chain reactions.
c. Allow scientists to examine thousands of genes all at once.
d. Decrease the time it takes for scientists to make copies of DNA.
3. Generally, every cell in our body contains the same 20,000 (or so) genes. However, cells in our body are different from each other because they:
a. Have different genes turned “on” or “off” to support different functions.
b. Contain different copies of genes for different functions.
c. Provide different nucleotide bases for each developmental function.
d. Function differently based on varying proteomics.
4. How can scientists determine the function of or differences between cell types? They can examine the:
a. Number of nucleotide bases in genes versus intergenetic sequences.
b. Amount of mRNA expressed for each gene in a cell type, and then compare that information between cell types.
c. Amount of mutations between genes in the intergenetic spaces.
d. Number of tRNA copies for a particular cell type.
5. How is a microarray constructed? In each spot, there are:
a. Copies of all the genes for an organism.
b. Multiple copies of one gene; each spot has copies for a different gene.
c. Multiple copies of intergenetic sequences, which bind to genes in the samples.
d. Copies of intergenetic sequences, which promote the replication of DNA in a sample.
6. The experiment that begins in Chapter 3 of the simulation seeks to answer the question:
a. What is the difference between intergenetic spaces in cancer cells versus healthy cells?
b. Why do different cell types express different amounts of mRNA?
c. How do different cancer cells produce different mutations?
d. What is the difference between healthy cells and cancer cells?
7. Why can’t doctors use cell appearance to diagnose cancer?
a. Not all cancer cells look different from healthy cells.
b. Cancer cells are too small to examine using cell appearance.
c. Not all cancer cells are able to be biopsied from the body.
d. Cancer cells change appearance when taken out of the body.
8. In the experiment, a solvent is added to each cell type (healthy cells and cancer cells). After the sample tube containing each cell type is mixed on the vortex, the RNA is separated from the rest of the sample in a centrifuge. Why does DNA settle to the bottom of the tube and RNA doesn’t?
a. RNA is much longer than DNA.
b. RNA is attached.
Introduction to Apollo: A webinar for the i5K Research CommunityMonica Munoz-Torres
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5K, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
This presentation is an introduction to Apollo for the members of the i5K Pilot Project Species.
The second part of a talk about hg and version control I gave to my colleagues in a group of bioinformaticians. First part here: http://www.slideshare.net/giovanni/hg-version-control-bioinformaticians
make is a basic tool to define pipelines of shell commands.
It is useful if you have many shell scripts and commands, and you want to organize them.
Even if it has been written to automatize the build of compiled language programs, make is also useful in bioinformatics and other fields.
This is a very short 30-minutes talk that I gave to a barcelona python developers meeting.
It explain a proposal to use doctest for biopython documentation (and in general, in bioinformatics).
It also contains an introduction and the use of automated build tools in bioinformatics, like make and scons.
Builder.ai Founder Sachin Dev Duggal's Strategic Approach to Create an Innova...Ramesh Iyer
In today's fast-changing business world, Companies that adapt and embrace new ideas often need help to keep up with the competition. However, fostering a culture of innovation takes much work. It takes vision, leadership and willingness to take risks in the right proportion. Sachin Dev Duggal, co-founder of Builder.ai, has perfected the art of this balance, creating a company culture where creativity and growth are nurtured at each stage.
GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using Deplo...James Anderson
Effective Application Security in Software Delivery lifecycle using Deployment Firewall and DBOM
The modern software delivery process (or the CI/CD process) includes many tools, distributed teams, open-source code, and cloud platforms. Constant focus on speed to release software to market, along with the traditional slow and manual security checks has caused gaps in continuous security as an important piece in the software supply chain. Today organizations feel more susceptible to external and internal cyber threats due to the vast attack surface in their applications supply chain and the lack of end-to-end governance and risk management.
The software team must secure its software delivery process to avoid vulnerability and security breaches. This needs to be achieved with existing tool chains and without extensive rework of the delivery processes. This talk will present strategies and techniques for providing visibility into the true risk of the existing vulnerabilities, preventing the introduction of security issues in the software, resolving vulnerabilities in production environments quickly, and capturing the deployment bill of materials (DBOM).
Speakers:
Bob Boule
Robert Boule is a technology enthusiast with PASSION for technology and making things work along with a knack for helping others understand how things work. He comes with around 20 years of solution engineering experience in application security, software continuous delivery, and SaaS platforms. He is known for his dynamic presentations in CI/CD and application security integrated in software delivery lifecycle.
Gopinath Rebala
Gopinath Rebala is the CTO of OpsMx, where he has overall responsibility for the machine learning and data processing architectures for Secure Software Delivery. Gopi also has a strong connection with our customers, leading design and architecture for strategic implementations. Gopi is a frequent speaker and well-known leader in continuous delivery and integrating security into software delivery.
LF Energy Webinar: Electrical Grid Modelling and Simulation Through PowSyBl -...DanBrown980551
Do you want to learn how to model and simulate an electrical network from scratch in under an hour?
Then welcome to this PowSyBl workshop, hosted by Rte, the French Transmission System Operator (TSO)!
During the webinar, you will discover the PowSyBl ecosystem as well as handle and study an electrical network through an interactive Python notebook.
PowSyBl is an open source project hosted by LF Energy, which offers a comprehensive set of features for electrical grid modelling and simulation. Among other advanced features, PowSyBl provides:
- A fully editable and extendable library for grid component modelling;
- Visualization tools to display your network;
- Grid simulation tools, such as power flows, security analyses (with or without remedial actions) and sensitivity analyses;
The framework is mostly written in Java, with a Python binding so that Python developers can access PowSyBl functionalities as well.
What you will learn during the webinar:
- For beginners: discover PowSyBl's functionalities through a quick general presentation and the notebook, without needing any expert coding skills;
- For advanced developers: master the skills to efficiently apply PowSyBl functionalities to your real-world scenarios.
State of ICS and IoT Cyber Threat Landscape Report 2024 previewPrayukth K V
The IoT and OT threat landscape report has been prepared by the Threat Research Team at Sectrio using data from Sectrio, cyber threat intelligence farming facilities spread across over 85 cities around the world. In addition, Sectrio also runs AI-based advanced threat and payload engagement facilities that serve as sinks to attract and engage sophisticated threat actors, and newer malware including new variants and latent threats that are at an earlier stage of development.
The latest edition of the OT/ICS and IoT security Threat Landscape Report 2024 also covers:
State of global ICS asset and network exposure
Sectoral targets and attacks as well as the cost of ransom
Global APT activity, AI usage, actor and tactic profiles, and implications
Rise in volumes of AI-powered cyberattacks
Major cyber events in 2024
Malware and malicious payload trends
Cyberattack types and targets
Vulnerability exploit attempts on CVEs
Attacks on counties – USA
Expansion of bot farms – how, where, and why
In-depth analysis of the cyber threat landscape across North America, South America, Europe, APAC, and the Middle East
Why are attacks on smart factories rising?
Cyber risk predictions
Axis of attacks – Europe
Systemic attacks in the Middle East
Download the full report from here:
https://sectrio.com/resources/ot-threat-landscape-reports/sectrio-releases-ot-ics-and-iot-security-threat-landscape-report-2024/
"Impact of front-end architecture on development cost", Viktor TurskyiFwdays
I have heard many times that architecture is not important for the front-end. Also, many times I have seen how developers implement features on the front-end just following the standard rules for a framework and think that this is enough to successfully launch the project, and then the project fails. How to prevent this and what approach to choose? I have launched dozens of complex projects and during the talk we will analyze which approaches have worked for me and which have not.
Epistemic Interaction - tuning interfaces to provide information for AI supportAlan Dix
Paper presented at SYNERGY workshop at AVI 2024, Genoa, Italy. 3rd June 2024
https://alandix.com/academic/papers/synergy2024-epistemic/
As machine learning integrates deeper into human-computer interactions, the concept of epistemic interaction emerges, aiming to refine these interactions to enhance system adaptability. This approach encourages minor, intentional adjustments in user behaviour to enrich the data available for system learning. This paper introduces epistemic interaction within the context of human-system communication, illustrating how deliberate interaction design can improve system understanding and adaptation. Through concrete examples, we demonstrate the potential of epistemic interaction to significantly advance human-computer interaction by leveraging intuitive human communication strategies to inform system design and functionality, offering a novel pathway for enriching user-system engagements.
UiPath Test Automation using UiPath Test Suite series, part 3DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 3. In this session, we will cover desktop automation along with UI automation.
Topics covered:
UI automation Introduction,
UI automation Sample
Desktop automation flow
Pradeep Chinnala, Senior Consultant Automation Developer @WonderBotz and UiPath MVP
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
PHP Frameworks: I want to break free (IPC Berlin 2024)Ralf Eggert
In this presentation, we examine the challenges and limitations of relying too heavily on PHP frameworks in web development. We discuss the history of PHP and its frameworks to understand how this dependence has evolved. The focus will be on providing concrete tips and strategies to reduce reliance on these frameworks, based on real-world examples and practical considerations. The goal is to equip developers with the skills and knowledge to create more flexible and future-proof web applications. We'll explore the importance of maintaining autonomy in a rapidly changing tech landscape and how to make informed decisions in PHP development.
This talk is aimed at encouraging a more independent approach to using PHP frameworks, moving towards a more flexible and future-proof approach to PHP development.
Accelerate your Kubernetes clusters with Varnish CachingThijs Feryn
A presentation about the usage and availability of Varnish on Kubernetes. This talk explores the capabilities of Varnish caching and shows how to use the Varnish Helm chart to deploy it to Kubernetes.
This presentation was delivered at K8SUG Singapore. See https://feryn.eu/presentations/accelerate-your-kubernetes-clusters-with-varnish-caching-k8sug-singapore-28-2024 for more details.
Essentials of Automations: Optimizing FME Workflows with ParametersSafe Software
Are you looking to streamline your workflows and boost your projects’ efficiency? Do you find yourself searching for ways to add flexibility and control over your FME workflows? If so, you’re in the right place.
Join us for an insightful dive into the world of FME parameters, a critical element in optimizing workflow efficiency. This webinar marks the beginning of our three-part “Essentials of Automation” series. This first webinar is designed to equip you with the knowledge and skills to utilize parameters effectively: enhancing the flexibility, maintainability, and user control of your FME projects.
Here’s what you’ll gain:
- Essentials of FME Parameters: Understand the pivotal role of parameters, including Reader/Writer, Transformer, User, and FME Flow categories. Discover how they are the key to unlocking automation and optimization within your workflows.
- Practical Applications in FME Form: Delve into key user parameter types including choice, connections, and file URLs. Allow users to control how a workflow runs, making your workflows more reusable. Learn to import values and deliver the best user experience for your workflows while enhancing accuracy.
- Optimization Strategies in FME Flow: Explore the creation and strategic deployment of parameters in FME Flow, including the use of deployment and geometry parameters, to maximize workflow efficiency.
- Pro Tips for Success: Gain insights on parameterizing connections and leveraging new features like Conditional Visibility for clarity and simplicity.
We’ll wrap up with a glimpse into future webinars, followed by a Q&A session to address your specific questions surrounding this topic.
Don’t miss this opportunity to elevate your FME expertise and drive your projects to new heights of efficiency.
Dev Dives: Train smarter, not harder – active learning and UiPath LLMs for do...UiPathCommunity
💥 Speed, accuracy, and scaling – discover the superpowers of GenAI in action with UiPath Document Understanding and Communications Mining™:
See how to accelerate model training and optimize model performance with active learning
Learn about the latest enhancements to out-of-the-box document processing – with little to no training required
Get an exclusive demo of the new family of UiPath LLMs – GenAI models specialized for processing different types of documents and messages
This is a hands-on session specifically designed for automation developers and AI enthusiasts seeking to enhance their knowledge in leveraging the latest intelligent document processing capabilities offered by UiPath.
Speakers:
👨🏫 Andras Palfi, Senior Product Manager, UiPath
👩🏫 Lenka Dulovicova, Product Program Manager, UiPath
UiPath Test Automation using UiPath Test Suite series, part 4DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 4. In this session, we will cover Test Manager overview along with SAP heatmap.
The UiPath Test Manager overview with SAP heatmap webinar offers a concise yet comprehensive exploration of the role of a Test Manager within SAP environments, coupled with the utilization of heatmaps for effective testing strategies.
Participants will gain insights into the responsibilities, challenges, and best practices associated with test management in SAP projects. Additionally, the webinar delves into the significance of heatmaps as a visual aid for identifying testing priorities, areas of risk, and resource allocation within SAP landscapes. Through this session, attendees can expect to enhance their understanding of test management principles while learning practical approaches to optimize testing processes in SAP environments using heatmap visualization techniques
What will you get from this session?
1. Insights into SAP testing best practices
2. Heatmap utilization for testing
3. Optimization of testing processes
4. Demo
Topics covered:
Execution from the test manager
Orchestrator execution result
Defect reporting
SAP heatmap example with demo
Speaker:
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
UiPath Test Automation using UiPath Test Suite series, part 4
Wagner chapter 5
1. Book club
Andreas Wagner,
The Origins of Evolutionary Innovations
Chapter 5
Book club presented by G. M. Dall'Olio,
Pompeu Fabra, IBE-CEXS
2. Reminder:
Genotype network
A genotype network is a set of genotypes that have the same
phenotype, and are connected by single pairwise differences
Green = same phenotype = a genotype network
Note: genotype network == neutral network
3. Chapter 5:
The Origins of Evolutionary
Innovations
This chapter makes some conclusions from the 4
preceding chapters
Under which common principle do metabolic
networks, regulatory circuits and protein/RNA
folds evolve?
Which are the basics of a theory of Innovation?
4. Many more genotypes than
phenotypes
Metabolic networks:
2 ^ S genotypes (S: number of known reactions)
2 ^ C phenotypes (C: number of carbon sources)
Regulatory Networks:
3 ^ N ^ 2 genotypes (3: activation, repression, no
interaction; N: number of reactions)
2 ^ S phenotypes (S: number of genes)
Protein molecules:
20 ^ S genotypes (S: length of sequence)
10 ^ 4 phenotypes (lattice protein folds)
5. Genotypes can vary a lot,
without altering the
phenotype
In metabolic networks, organisms can differ for
75% of reactions, but still have the same
phenotype
Some regulatory circuits can be completely
different but still have the same functions
(examples of GAL4 in C.albicans/S.cerevisiae,
etc..)
Proteins with different sequences can have the same
fold (e.g. globins, etc..)
6. Genotypes can vary a lot,
without altering the
phenotype
Same fold but different sequence (genotype
Distance = 1.0):
http://eterna.cmu.edu/
7. The same phenotype can be
achieved by many
genotypes
A corollary of the previous two slides is that the
same phenotype can be achieved by many
genotypes
Why should a phenotype be reachable by more than
one genotype? (open question)
8. Robustness of a genotype
network
The robustness of a biological system is its ability
to withstand changes without altering the
phenotype
Not only within a genotype network. It is also
important that the neighbors of points in a
genotype network have “neutral” phenotypes
e.g. the neighbor of a genotype must be viable
9. The genotype-phenotype
function
The genotypephenotype function is a function that
allows to predict the phenotype of certain
genotype
Flux balance analysis in metabolic networks
Structure prediction in sequence networks
...
10. Definitions: The Genotype-
Phenotype-Map
The method of representing all genotypes as a Hamming graph and defining neutral
networks is also called “GenotypePhenotypeMap”
I am not sure about who invented the method, but it is well described in [1]
[1] Stadler, B.M. et al., 2001. The topology of the possible: formal spaces underlying patterns of evolutionary change.
Journal of theoretical biology, 213(2), pp.241-74.
11. The genotype space is huge
For a protein of length 10, there are 20^10 possible
sequences
It is difficult for humans to imagine how much the
genotype space is big
12. Big genotype networks can
be still small compared to
the genotype space
A given RNA structure can be generated by
5*10^22 sequences
Yet, this is only a tiny fraction of the genotype
space
13. Big genotype networks are
favored by evolution
Imagine that a given biological function can be
carried out by two different phenotypes:
Phenotype 1 has a big genotype network
Phenotype 2 has a small genotype network
Selection will be more likely to find Phenotype 1,
just because there are more genotypes that
produce it
14. Small and big genotype
networks
The two purple
phenotypes have a
selective advantage
over white ones
However, evolution is
more likely to find
the light phenotype,
because its genotype
network is bigger
15. Phenotypes with small
genotype networks can be
important
We said that big genotype networks are more likely
to be found by evolution
However, in nature we can observe phenotypes
with small genotype networks
16. Phenotypes involved in
multiple functions can still
have big genotype networks
Some systems can carry out more than one
biological function
For example, many metabolisms can survive on both
glucose and mannose
The genotype network of these systems would be
the intersection of the genotype networks that
carry each of the functions
Yet, these genotype networks are still big
17. Intersection of genotype
networks
Yellow → can 0....0 ….. ….. ….. ….. …..
survive on 0....1 ….. ….. ….. ….. …..
Glucose as sole 0...10 ….. ….. ….. ….. …..
0..1.0 ….. ….. …..
carbon source 0.1..0 ….. ….. …..
Blue → can survive 0..... ….. ….. …..
on Alanine as ….. ….. …..
….. ….. …..
sole carbon
….. ….. …..
source ….. ….. ….. …..
Green → ….. ….. ….. ….. ….. …..
intersection ….. ….. ….. ….. ….. …..
….. ….. ….. ….. ….. …..
18. Connectivity and broadness
of genotype networks
Two important properties of genotype networks are
the connectivity and the broadness
These two properties are important in the search for
innovations
19. A poorly connected
genotype set
Fig a shows a set of notconnected
genotype networks
They all have the same phenotype,
but are not connected
In this situation, populations can not
explore the genotype space
efficiently, because they don't
have a way to “jump” between
genotype networks
(recombination and
chromosomal
arrangements will be
discussed later)
20. A well connected but
localized genotype network
Fig b shows a well connected
genotype network
However, this network is clustered,
and all its nodes are close
It is difficult for a population to find
Innovations, because there is no
way to get close to them
21. A connected and broad
genotype network
Fig c represents a well connected and
broad genotype network
This is the ideal situation for finding
innovations
A population can explore the
genotype space without having to
“jump”
23. Genotype networks are
highly interwoven
Genotype networks are usually close in the space
Many organisms can survive on multiple carbon
sources
It is possible to convert RNA structures by changing
few aminoacids
24. Genotype networks are
highly interwoven
Yellow → can 0....0 ….. ….. ….. ….. …..
survive on 0....1 ….. ….. ….. ….. …..
Glucose as sole 0...10 ….. ….. ….. ….. …..
0..1.0 ….. ….. …..
carbon source 0.1..0 ….. ….. …..
Blue → can survive 0..... ….. ….. …..
on Alanine as ….. ….. …..
….. ….. …..
sole carbon
….. ….. …..
source ….. ….. ….. …..
Green → ….. ….. ….. ….. ….. …..
intersection ….. ….. ….. ….. ….. …..
….. ….. ….. ….. ….. …..
25. The theory of innovation
In this chapter, Wagner formalizes the framework
of “genotypephenotypemaps” for studying how
innovations can be found
It also describe some important properties that a
system must have in order to reach innovations
26. The theory of Innovations
Innovation is combinatorial in nature
Genotypephenotypemaps allow to explore the
nature of innovations
Genotypes have many neighbors with the same
phenotype
Many or all genotypes with the same phenotype are
connected in genotype networks
27. The theory of Innovations
Genotype networks of different phenotypes are
different in size
Typical genotype networks traverse a large part of
genotype space
Different neighborhoods of a genotype network
contain different phenotypes
28. Pros of this theory of
innovation
Genotype networks can explain how population
explore the genotype space, without altering the
phenotype
This framework is valid for metabolic networks,
regulatory circuits and sequences
Captures the combinatorial nature of innovation
It allows to simulate that a problem can be solved
through different solutions
e.g. different metabolic networks can survive on
glucose
29. Cons of this theory of
Innovation
Difficult to get to phenotypes that are highly
innovative, but have a tiny genotype network
Difficult to study systems where genotype networks
are not connected or localized
The method doesn't work if there are more
phenotypes than genotypes (phenotipic plasticity)
Immunity systems tend to have more phenotypes
than genotypes
30. Take Home messages
We have seen some properties that are common for
the evolution of metabolic networks, regulatory
circuits and sequences
The framework of genotypephenotypemaps can
be used to explore how innovations are found
31. There are many more
genotypes than phenotypes
A common property of the systems studied in the
previous chapters is that there are more genotypes
than phenotypes