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6.5D: Web, Network, and Ring of Life Models - Biology

6.5D: Web, Network, and Ring of Life Models - Biology


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To more accurately describe the phylogenetic relationships of life, web and ring models have been proposed as updates to tree models.

Learning Objectives

  • Describe the web, network, and ring of life models of phylogenetic trees

Key Points

  • A phylogenetic model that resembles a web or a network was proposed since eukaryotes evolved not from a single prokaryotic ancestor, but from a pool of many species that were sharing genes by HGT mechanisms.
  • A phylogenetic model that resembles a ring was proposed in which species of all three domains, Archaea, Bacteria, and Eukarya, evolved from a single pool of gene-swapping prokaryotes.
  • Phylogenetic models will continue to evolve as phylogeneticists remain highly skeptical of the current tree, web, and ring models.

Key Terms

  • web of life: a phylogenetic model that resembles a web or a network more than a tree
  • ring of life: a phylogenetic model where all three domains of life (Archaea, Bacteria, and Eukarya) evolved from a pool of primitive prokaryotes

The recognition of the importance of Horizontal gene transfer (HGT), especially in the evolution of prokaryotes, has caused some to propose abandoning the classic “tree of life” model. In 1999, a phylogenetic model that resembles a web or a network more than a tree was proposed. The hypothesis is that eukaryotes evolved not from a single prokaryotic ancestor, but from a pool of many species that were sharing genes by HGT mechanisms. Some individual prokaryotes were responsible for transferring the bacteria that caused mitochondrial development in the new eukaryotes, whereas other species transferred the bacteria that gave rise to chloroplasts. This model is often called the “web of life.” In an effort to save the tree analogy, some have proposed using the Ficus tree with its multiple trunks as a phylogenetic tree to represent the evolutionary role for HGT.

Others have proposed abandoning any tree-like model of phylogeny in favor of a ring structure. The ” ring of life ” is a phylogenetic model where all three domains of life evolved from a pool of primitive prokaryotes. Using the conditioned reconstruction algorithm, it proposes a ring-like model in which species of all three domains (Archaea, Bacteria, and Eukarya) evolved from a single pool of gene-swapping prokaryotes. This structure is proposed as the best fit for data from extensive DNA analyses; the ring model is the only one that adequately takes HGT and genomic fusion into account. However, phylogeneticists remain highly skeptical of this model.

In summary, the “tree of life” model proposed by Darwin must be modified to include HGT. This does not mean a tree, web, or a ring will correlate completely to an accurate description of phylogenetic relationships of life. A consequence of the new thinking about phylogenetic models is the idea that Darwin’s original conception of the phylogenetic tree is too simple, but made sense based on what was known at that time.


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6.5D: Web, Network, and Ring of Life Models - Biology

-Transmits data, instructions and information in both direction

-Only one device can transfer items at one time

-A cable forms a closed ring, or a loop, with all computers and devices arranged along the ring

-Data transmitted from the device to another around the entires ring in one direction

-Used primarily for LANs, but is also used to connect a mainframe to a WAN

-All data that transfer from one computer to another passes through the central computer

-if a device on a ring network fails, those devices after the failed device cannot function

  1. Explain the term upload [ 1 /2 mark]
    Storing a file into a web server
  2. If a 56K modem is operating at full speed, how long does it take to download a 1-MBfile? [2 marks]
    1 MB÷ 56 Kbps = (220× 8) bits÷ (56× 103) bps
    = 149.8 s
    1. Describe the role of the systems analyst. [2 marks]
      A systems analyst observes, clarifies and models an existing systemwith a view to improving it through computerization
    2. Describe 2 techniques used by the systems analyst in requirements specification.[2 marks]
      Interviewing those involved with current system
      Observing how the current system operates
      Identifying the data requirements and the data flow of the current system.
    3. In the software development process, what happens at the analysis stage? [1 Mark]
      At the analysis stage, the system analyst and the person requesting the software get together to clarify the problem and identify in detail what the solution must provide.
    4. Describe fully what is meant by the term top-down design? [3 Marks]
      The problem is set out at the top level as a series of large steps.
      Each step is then broken down further until at the bottom level, each small step describes a single task.
      Each task can be easily coded into the required programming language.
    5. The process of developing such software is an iterative process. What does iterative mean?[1 Mark]
      Iteration means that some of the steps in the development process may have to be repeated. At each stage, new details about the problem may emerge, the client may request a slight change, a technological innovation may have to be incorporated, or a error may be detected. The systems analyst will go back through all the previous stages to check that they are still valid and correct.)
      1. What are CASE tools? [1 Mark]
        Software tools for each stage of the software development process.
      2. What is the purpose of CASE tools? [1 Mark]
        They speed up the SD process by automating some of the activities
      3. What does CASE stand for? [1 Mark]
        Computer Aided Software Engineering
        1. Describe four functions of a single user operating system. [4 Marks]
          • Memory management &ndash ensuring one program does not overwrite another and that there is enough space to load a file, etc
          • File management &ndash the organisation of data and program files on backing storage
          • Input &ndash output &ndash to manage I/O and to ensure differences in system devices are compensated for
          • Process management &ndash order of processing of tasks in CPU.
        2. Explain the need for an operating system to have a command language interpreter. [1 Mark]
          The command language interpreter converts the commands entered by the user to binary , interprets them and passes them on to the appropriate sub-system within the OS for action .
        3. Give 4 examples of the many processes which can be initiated by a user and which are then carried out by the operating system. [4 Marks]
          • Load file from backing store
          • Print file
          • Save data file to backing store
          • Execute a program file after loading to RAM
        4. What happens if a command entered by the user is not recognized by the operating system? [1 Mark]
          If the user enters an invalid command or enters a command with a syntax error then the CLI reports that error to the user, usually through a dialogue box.
        5. Describe an advantage and a disadvantage to storing the operating system in RAM rather than in ROM?
          Advantage: computer manufacturer can issue operating system updates very easily so that computer users do not need to be always buying new systems
          Disadvantage: OS may be overwritten or corrupted by mistake
        6. Describe three features that a networkoperatingsystem must have that a single user operating system does not need.[3 Marks]
          A network OS must ensure data integrity in data transfer across the network
          A network OS must allow multi-user access
          A network OS must be able to set access rights for different users
          1. Explain two reasons why computers use the binary system? [2 Marks]
            Binary arithmetic is simple to implement because there are only 2 digits and 4 arithmetic rules.
            Electronic circuitry has only two voltage levels, pulse or no pulse, so it is easy to distinguish between 0 and 1.
          2. What is meant by the term word in the phrase 16-bit word computer? [1 Mark]
            A word is the amount of data that is handled by the processor in a single operation, in this case, 16 bits or 2 bytes.
          3. What is the decimal value of the largest integer that can be represented by a byte in a computer which deals only with positive numbers? [1 Mark]
            255 or (2^ 8 &ndash 1 ). (Remember that one of the 256 bit patterns is for zero.)
          4. What does the acronym ASCII stand for and what is ASCII? [2 Marks]
            American Standard Code for Information Interchange.
            ASCII is a binary code that gives each character and symbol on the keyboard a unique binary code. It allows computers to handle text.
          5. Carry out the following binary arithmetic: [3 marks]
            1. 11+11
              11
              +11
              100
            2. 11 X 11
              11
              X11
              11
              11
              1001
            3. 110/11

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            DISCUSSION

            Our work establishes the developing germline cyst as a model of collective dynamics in small cell clusters, in a highly reproducible setting where all cells are uniquely identifiable. We uncovered an emergent pattern of cell sizes and presented a plausible model that captures the most salient features of egg chamber growth and correctly predicts several features of collective growth associated with multicellular systems. However, our model is clearly 𠇊 simplification and an idealization, and consequently a falsification” ([27], p. 37) of dynamics in real egg chambers. Future studies can capitalize on the model’s simplicity and include additional features, such as the non-uniform distribution of ring canal sizes, the effects of hormonal regulation, and somagermline interactions [7, 13, 28�]. It is also critical to identify the limiting factor (or factors) that control cell-size increase in our model. We expect these factors, be they nutrients or organelles (such as ribosomes), to be sensitive to microtubule transport, as genetic and pharmacological perturbations of the microtubule network disrupt the normal pattern of cell sizes [6, 22, 25].

            Our model of a small cell cluster displays common features of collective growth on organismal scale: parts diverge in size as the whole system grows, and sizes of the constitutive parts relate allometrically. While such complex spatiotemporal patterns during organismal growth have been documented since Thompson’s and Huxley’s studies [31, 32], the underlying mechanisms have remained largely unclear [3]. Studies in model organisms have suggested two possible classes of mechanisms for differential growth. The first class relies on intrinsic differences between growing parts, such as differential expression of selector genes [33]. The second class relies on interactions between growing parts, such as their competition for resources [34]. While our model for the emergence of a non-uniform distribution of cell sizes in the egg chamber cannot rule out the first class of mechanisms of differential growth, it most closely aligns with the second, presumably resulting from competition between the growing parts for resources and their non-uniform allocation and transport.