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Sunday, August 20, 2023

History of free and open-source software

In the 1950s and 1960s, computer operating software and compilers were delivered as a part of hardware purchases without separate fees. At the time, source code, the human-readable form of software, was generally distributed with the software providing the ability to fix bugs or add new functions.[1] Universities were early adopters of computing technology. Many of the modifications developed by universities were openly shared, in keeping with the academic principles of sharing knowledge, and organizations sprung up to facilitate sharing. As large-scale operating systems matured, fewer organizations allowed modifications to the operating software, and eventually such operating systems were closed to modification. However, utilities and other added-function applications are still shared and new organizations have been formed to promote the sharing of software.

Sharing techniques before software

The concept of free sharing of technological information existed long before computers. For example, in the early years of automobile development, one enterprise owned the rights to a 2-cycle gasoline engine patent originally filed by George B. Selden. By controlling this patent, they were able to monopolize the industry and force car manufacturers to adhere to their demands, or risk a lawsuit. In 1911, independent automaker Henry Ford won a challenge to the Selden patent. The result was that the Selden patent became virtually worthless and a new association (which would eventually become the Motor Vehicle Manufacturers Association) was formed. The new association instituted a cross-licensing agreement among all US auto manufacturers: although each company would develop technology and file patents, these patents were shared openly and without the exchange of money between all the manufacturers. By the time the US entered World War 2, 92 Ford patents and 515 patents from other companies were being shared between these manufacturers, without any exchange of money (or lawsuits).

Free software before the 1980s

In the 1950s and into the 1960s almost all software was produced by academics and corporate researchers working in collaboration, often shared as public-domain software. As such, it was generally distributed under the principles of openness and cooperation long established in the fields of academia, and was not seen as a commodity in itself. Such communal behavior later became a central element of the so-called hacking culture (a term with a positive connotation among open-source programmers). At this time, source code, the human-readable form of software, was generally distributed with the software machine code because users frequently modified the software themselves, because it would not run on different hardware or OS without modification, and also to fix bugs or add new functions. The first example of free and open-source software is believed to be the A-2 system, developed at the UNIVAC division of Remington Rand in 1953, which was released to customers with its source code. They were invited to send their improvements back to UNIVAC. Later, almost all IBM mainframe software was also distributed with source code included. User groups such as that of the IBM 701, called SHARE, and that of Digital Equipment Corporation (DEC), called DECUS, were formed to facilitate the exchange of software. The SHARE Operating System, originally developed by General Motors, was distributed by SHARE for the IBM 709 and 7090 computers. Some university computer labs even had a policy requiring that all programs installed on the computer had to come with published source-code files.

In 1969 the Advanced Research Projects Agency Network (ARPANET), a transcontinental, high-speed computer network was constructed. The network (later succeeded by the Internet) simplified the exchange of software code.

Some free software which was developed in the 1970s continues to be developed and used, such as TeX (developed by Donald Knuth) and SPICE.

Initial decline of free software

By the late 1960s change was coming: as operating systems and programming language compilers evolved, software production costs were dramatically increasing relative to hardware. A growing software industry was competing with the hardware manufacturers' bundled software products (the cost of bundled products was included in the hardware cost), leased machines required software support while providing no revenue for software, and some customers, able to better meet their own needs, did not want the costs of the manufacturer's software to be bundled with hardware product costs. In the United States vs. IBM antitrust suit, filed 17 January 1969, the U.S. government charged that bundled software was anticompetitive. While some software continued to come at no cost, there was a growing amount of software that was for sale only under restrictive licenses.

In the early 1970s AT&T distributed early versions of Unix at no cost to the government and academic researchers, but these versions did not come with permission to redistribute or to distribute modified versions, and were thus not free software in the modern meaning of the phrase. After Unix became more widespread in the early 1980s, AT&T stopped the free distribution and charged for system patches. As it is quite difficult to switch to another architecture, most researchers paid for a commercial license.

Software was not considered copyrightable before the 1974 US Commission on New Technological Uses of Copyrighted Works (CONTU) decided that "computer programs, to the extent that they embody an author's original creation, are proper subject matter of copyright". Therefore, software had no licenses attached and was shared as public-domain software, typically with source code. The CONTU decision plus later court decisions such as Apple v. Franklin in 1983 for object code, gave computer programs the copyright status of literary works and started the licensing of software and the shrink-wrap closed source software business model.

In the late 1970s and early 1980s, computer vendors and software-only companies began routinely charging for software licenses, marketing software as "Program Products" and imposing legal restrictions on new software developments, now seen as assets, through copyrights, trademarks, and leasing contracts. In 1976 Bill Gates wrote an essay entitled "Open Letter to Hobbyists", in which he expressed dismay at the widespread sharing of Microsoft's product Altair BASIC by hobbyists without paying its licensing fee. In 1979, AT&T began to enforce its licenses when the company decided it might profit by selling the Unix system. In an announcement letter dated 8 February 1983 IBM inaugurated a policy of no longer distributing sources with purchased software.

To increase revenues, a general trend began to no longer distribute source code (easily readable by programmers), and only distribute the executable machine code that was compiled from the source code. One person especially distressed by this new practice was Richard Stallman. He was concerned that he could no longer study or further modify programs initially written by others. Stallman viewed this practice as ethically wrong. In response, he founded the GNU Project in 1983 so that people could use computers using only free software. He established a non-profit organization, the Free Software Foundation, in 1985, to more formally organize the project. He invented copyleft, a legal mechanism to preserve the "free" status of a work subject to copyright, and implemented this in the GNU General Public License. Copyleft licenses allow authors to grant a number of rights to users (including rights to use a work without further charges, and rights to obtain, study and modify the program's complete corresponding source code) but requires derivatives to remain under the same license or one without any additional restrictions. Since derivatives include combinations with other original programs, downstream authors are prevented from turning the initial work into proprietary software, and invited to contribute to the copyleft commons. Later, variations of such licenses were developed by others.

1980s and 1990s

Informal software sharing continues

However, there were still those who wished to share their source code with other programmers and/or with users on a free basis, then called "hobbyists" and "hackers". Before the introduction and widespread public use of the internet, there were several alternative ways available to do this, including listings in computer magazines (like Dr. Dobb's Journal, Creative Computing, SoftSide, Compute!, Byte, etc.) and in computer programming books, like the bestseller BASIC Computer Games. Though still copyrighted, annotated source code for key components of Atari 8-bit family system software was published in mass market books, including The Atari BASIC Source Book (full source for Atari BASIC) and Inside Atari DOS (full source for Atari DOS).

SHARE program library

The SHARE users group, founded in 1955, began collecting and distributing free software. The first documented distribution from SHARE was dated 17 October 1955. The "SHARE Program Library Agency" (SPLA) distributed information and software, notably on magnetic tape.

DECUS tapes

In the early 1980s, the so-called DECUS tapes were a worldwide system for the transmission of free software for users of DEC equipment. Operating systems were usually proprietary software, but many tools like the TECO editor, Runoff text formatter, or List file listing utility, etc. were developed to make users' lives easier, and distributed on the DECUS tapes. These utility packages benefited DEC, which sometimes incorporated them into new releases of their proprietary operating system. Even compilers could be distributed and for example Ratfor (and Ratfiv) helped researchers to move from Fortran coding to structured programming (suppressing the GO TO statement). The 1981 Decus tape was probably the most innovative by bringing the Lawrence Berkeley Laboratory Software Tools Virtual Operating System which permitted users to use a Unix-like system on DEC 16-bit PDP-11s and 32-bit VAXes running under the VMS operating system. It was similar to the current cygwin system for Windows. Binaries and libraries were often distributed, but users usually preferred to compile from source code.

Online software sharing communities in the 1980s

In the 1980s, parallel to the free software movement, software with source code was shared on BBS networks. This was sometimes a necessity; software written in BASIC and other interpreted languages could only be distributed as source code, and much of it was freeware. When users began gathering such source code, and setting up boards specifically to discuss its modification, this was a de facto open-source system.

One of the most obvious examples of this is one of the most-used BBS systems and networks, WWIV, developed initially in BASIC by Wayne Bell. A culture of "modding" his software, and distributing the mods, grew up so extensively that when the software was ported to first Pascal, then C++, its source code continued to be distributed to registered users, who would share mods and compile their own versions of the software. This may have contributed to it being a dominant system and network, despite being outside the Fidonet umbrella that was shared by so many other BBS makers.

Meanwhile, the advent of Usenet and UUCPNet in the early 1980s further connected the programming community and provided a simpler way for programmers to share their software and contribute to software others had written.

Launch of the free software movement

In 1983, Richard Stallman launched the GNU Project to write a complete operating system free from constraints on use of its source code. Particular incidents that motivated this include a case where an annoying printer couldn't be fixed because the source code was withheld from users. Stallman also published the GNU Manifesto in 1985 to outline the GNU Project's purpose and explain the importance of free software. Another probable inspiration for the GNU project and its manifesto was a disagreement between Stallman and Symbolics, Inc. over MIT's access to updates Symbolics had made to its Lisp machine, which was based on MIT code. Soon after the launch, he used the existing term "free software" and founded the Free Software Foundation to promote the concept. The Free Software Definition was published in February 1986.

In 1989, the first version of the GNU General Public License was published. A slightly updated version 2 was published in 1991. In 1989, some GNU developers formed the company Cygnus Solutions. The GNU project's kernel, later called "GNU Hurd", was continually delayed, but most other components were completed by 1991. Some of these, especially the GNU Compiler Collection, had become market leaders in their own right. The GNU Debugger and GNU Emacs were also notable successes.

Linux (1991–present)

The Linux kernel, started by Linus Torvalds, was released as freely modifiable source code in 1991. The license was not a free software license, but with version 0.12 in February 1992, Torvalds relicensed the project under the GNU General Public License. Much like Unix, Torvalds' kernel attracted attention from volunteer programmers.

Until this point, the GNU project's lack of a kernel meant that no complete free software operating systems existed. The development of Torvalds' kernel closed that last gap. The combination of the almost-finished GNU operating system and the Linux kernel made the first complete free software operating system.

Among Linux distributions, Debian GNU/Linux, begun by Ian Murdock in 1993, is noteworthy for being explicitly committed to the GNU and FSF principles of free software. The Debian developers' principles are expressed in the Debian Social Contract. Since its inception, the Debian project has been closely linked with the FSF, and in fact was sponsored by the FSF for a year in 1994–1995. In 1997, former Debian project leader Bruce Perens also helped found Software in the Public Interest, a non-profit funding and support organization for various free software projects.

Since 1996, the Linux kernel has included proprietary licensed components, so that it was no longer entirely free software. Therefore, the Free Software Foundation Latin America released in 2008 a modified version of the Linux-kernel called Linux-libre, where all proprietary and non-free components were removed.

Many businesses offer customized Linux-based products, or distributions, with commercial support. The naming remains controversial. Referring to the complete system as simply "Linux" is common usage. However, the Free Software Foundation, and many others, advocate the use of the term "GNU/Linux", saying that it is a more accurate name for the whole operating system.

Linux adoption grew among businesses and governments in the 1990s and 2000s. In the English-speaking world at least, Ubuntu and its derivatives became a relatively popular group of Linux distributions.

The free BSDs (1993–present)

When the USL v. BSDi lawsuit was settled out of court in 1993, FreeBSD and NetBSD (both derived from 386BSD) were released as free software. In 1995, OpenBSD forked from NetBSD. In 2004, Dragonfly BSD forked from FreeBSD.

The dot-com years (late 1990s)

In the mid to late 90s, when many website-based companies were starting up, free software became a popular choice for web servers. The Apache HTTP Server became the most-used web-server software, a title that still holds as of 2015. Systems based on a common "stack" of software with the Linux kernel at the base, Apache providing web services, the MySQL database engine for data storage, and the PHP programming language for providing dynamic pages, came to be termed LAMP systems. In actuality, the programming language that predated PHP and dominated the web in the mid and late 1990s was Perl. Web forms were processed on the server side through Common Gateway Interface scripts written in Perl.

The term "open source," as related to free software, was in common use by 1995. Other recollection have it in use during the 1980s.

The launch of Open Source

In 1997, Eric S. Raymond published "The Cathedral and the Bazaar", a reflective analysis of the hacker community and free software principles. The paper received significant attention in early 1998 and was one factor in motivating Netscape Communications Corporation to release their popular Netscape Communicator Internet suite as free software.

Netscape's act prompted Raymond and others to look into how to bring free software principles and benefits to the commercial-software industry. They concluded that FSF's social activism was not appealing to companies like Netscape, and looked for a way to rebrand the free software movement to emphasize the business potential of the sharing of source code.

The label "open source" was adopted by some people in the free software movement at a strategy session held at Palo Alto, California, in reaction to Netscape's January 1998 announcement of a source code release for Navigator. The group of individuals at the session included Christine Peterson who suggested "open source", Todd Anderson, Larry Augustin, Jon Hall, Sam Ockman, Michael Tiemann, and Eric S. Raymond. Over the next week, Raymond and others worked on spreading the word. Linus Torvalds gave an all-important sanction the following day. Phil Hughes offered a pulpit in Linux Journal. Richard Stallman, pioneer of the free software movement, flirted with adopting the term, but changed his mind. Those people who adopted the term used the opportunity before the release of Navigator's source code to free themselves of the ideological and confrontational connotations of the term "free software". Netscape released its source code under the Netscape Public License and later under the Mozilla Public License.

The term was given a big boost at an event organized in April 1998 by technology publisher Tim O'Reilly. Originally titled the "Freeware Summit" and later named the "Open Source Summit", the event brought together the leaders of many of the most important free and open-source projects, including Linus Torvalds, Larry Wall, Brian Behlendorf, Eric Allman, Guido van Rossum, Michael Tiemann, Paul Vixie, Jamie Zawinski of Netscape, and Eric Raymond. At that meeting, the confusion caused by the name free software was brought up. Tiemann argued for "sourceware" as a new term, while Raymond argued for "open source". The assembled developers took a vote, and the winner was announced at a press conference that evening. Five days later, Raymond made the first public call to the free software community to adopt the new term. The Open Source Initiative was formed shortly thereafter. According to the OSI Richard Stallman initially flirted with the idea of adopting the open source term. But as the enormous success of the open source term buried Stallman's free software term and his message on social values and computer users' freedom, later Stallman and his FSF strongly objected to the OSI's approach and terminology. Due to Stallman's rejection of the term "open-source software", the FOSS ecosystem is divided in its terminology; see also Alternative terms for free software. For example, a 2002 FOSS developer survey revealed that 32.6% associated themselves with OSS, 48% with free software, and 19.4% in between or undecided. Stallman still maintained, however, that users of each term were allies in the fight against proprietary software.

On 13 October 2000, Sun Microsystems released the StarOffice office suite as free software under the GNU Lesser General Public License. The free software version was renamed OpenOffice.org, and coexisted with StarOffice.

By the end of the 1990s, the term "open source" gained much traction in public media and acceptance in software industry in context of the dotcom bubble and the open-source software driven Web 2.0.

Desktop (1984–present)

A historical example of graphical user interface and applications common to the MIT X Consortium's distribution running under the twm window manager: X Terminal, Xbiff, xload and a graphical manual page browser

The X Window System was created in 1984, and became the de facto standard window system in desktop free software operating systems by the mid-1990s. X runs as a server, and is responsible for communicating with graphics hardware on behalf of clients (which are individual software applications). It provides useful services such as having multiple virtual desktops for the same monitor, and transmitting visual data across the network so a desktop can be accessed remotely.

Initially, users or system administrators assembled their own environments from X and available window managers (which add standard controls to application windows; X itself does not do this), pagers, docks and other software. While X can be operated without a window manager, having one greatly increases convenience and ease of use.

Two key "heavyweight" desktop environments for free software operating systems emerged in the 1990s that were widely adopted: KDE and GNOME. KDE was founded in 1996 by Matthias Ettrich. At the time, he was troubled by the inconsistencies in the user interfaces of UNIX applications. He proposed a new desktop environment. He also wanted to make this desktop easy to use. His initial Usenet post spurred a lot of interest.

Ettrich chose to use the Qt toolkit for the KDE project. At the time, Qt did not use a free software license. Members of the GNU project became concerned with the use of such a toolkit for building a free software desktop environment. In August 1997, two projects were started in response to KDE: the Harmony toolkit (a free replacement for the Qt libraries) and GNOME (a different desktop without Qt and built entirely on top of free software). GTK+ was chosen as the base of GNOME in place of the Qt toolkit.

In November 1998, the Qt toolkit was licensed under the free/open source Q Public License (QPL) but debate continued about compatibility with the GNU General Public License (GPL). In September 2000, Trolltech made the Unix version of the Qt libraries available under the GPL, in addition to the QPL, which has eliminated the concerns of the Free Software Foundation. KDE has since been split into KDE Plasma Workspaces, a desktop environment, and KDE Software Compilation, a much broader set of software that includes the desktop environment.

Both KDE and GNOME now participate in freedesktop.org, an effort launched in 2000 to standardize Unix desktop interoperability, although there is still competition between them.

Since 2000, software written for X almost always uses some widget toolkit written on top of X, like Qt or GTK.

In 2010, Canonical released the first version of Unity, a replacement for the prior default desktop environment for Ubuntu, GNOME. This change to a new, under-development desktop environment and user interface was initially somewhat controversial among Ubuntu users.

In 2011, GNOME 3 was introduced, which largely discarded the desktop metaphor in favor of a more mobile-oriented interface. The ensuing controversy led Debian to consider making the Xfce environment default on Debian 7. Several independent projects were begun to keep maintaining the GNOME 2 code.

Fedora did not adopt Unity, retaining its existing offering of a choice of GNOME, KDE and LXDE with GNOME being the default, and hence Red Hat Enterprise Linux (for which Fedora acts as the "initial testing ground") did not adopt Unity either. A fork of Ubuntu was made by interested third-party developers that kept GNOME and discarded Unity. In March 2017, Ubuntu announced that it will be abandoning Unity in favour of GNOME 3 in future versions, and ceasing its efforts in developing Unity-based smartphones and tablets.

When Google built the Linux-based Android operating system, mostly for phone and tablet devices, it replaced X with the purpose-built SurfaceFlinger.

Open-source developers also criticized X as obsolete, carrying many unused or overly complicated elements in its protocol and libraries, while missing modern functionality, e.g., compositing, screen savers, and functions provided by window managers. Several attempts have been made or are underway to replace X for these reasons, including:

  • The Y Window System, which had ceased development by 2006.
  • The Wayland project, started in 2008.
  • The Mir project, started in 2013 by Canonical Ltd. to produce a replacement windowing system for Ubuntu.

Microsoft, SCO and other attacks (1998–2014)

As free software became more popular, industry incumbents such as Microsoft started to see it as a serious threat. This was shown in a leaked 1998 document, confirmed by Microsoft as genuine, which came to be called the first of the Halloween Documents.

Steve Ballmer once compared the GPL to "a cancer", but has since stopped using this analogy. Indeed, Microsoft has softened its public stance towards open source in general, with open source since becoming an important part of the Microsoft Windows ecosystem. However, at the same time, behind the scenes, Microsoft's actions have been less favourable toward the open-source community.

SCO v. IBM and related bad publicity (2003–present)

In 2003, a proprietary Unix vendor and former Linux distribution vendor called SCO alleged that Unix intellectual property had been inappropriately copied into the Linux kernel, and sued IBM, claiming that it bore responsibility for this. Several related lawsuits and countersuits followed, some originating from SCO, some from others suing SCO. However, SCO's allegations lacked specificity, and while some in the media reported them as credible, many critics of SCO believed the allegations to be highly dubious at best.

Over the course of the SCO v. IBM case, it emerged that not only had SCO been distributing the Linux kernel for years under the GPL, and continued to do so (thus rendering any claims hard to sustain legally), but that SCO did not even own the copyrights to much of the Unix code that it asserted copyright over, and had no right to sue over them on behalf of the presumed owner, Novell.

This was despite SCO's CEO, Darl McBride, having made many wild and damaging claims of inappropriate appropriation to the media, many of which were later shown to be false, or legally irrelevant even if true.

The blog Groklaw was one of the most forensic examiners of SCO's claims and related events, and gained its popularity from covering this material for many years.

SCO suffered defeat after defeat in SCO v. IBM and its various other court cases, and filed for Chapter 11 bankruptcy in 2007. However, despite the courts finding that SCO did not own the copyrights (see above), and SCO's lawsuit-happy CEO Darl McBride no longer running the company, the bankruptcy trustee in charge of SCO-in-bankruptcy decided to press on with some portions he claimed remained relevant in the SCO v. IBM lawsuit. He could apparently afford to do this because SCO's main law firm in SCO v. IBM had signed an agreement at the outset to represent SCO for a fixed amount of money no matter how long the case took to complete.

In 2004, the Alexis de Tocqueville Institution (ADTI) announced its intent to publish a book, Samizdat: And Other Issues Regarding the 'Source' of Open Source Code, showing that the Linux kernel was based on code stolen from Unix, in essence using the argument that it was impossible to believe that Linus Torvalds could produce something as sophisticated as the Linux kernel. The book was never published, after it was widely criticised and ridiculed, including by people supposedly interviewed for the book. It emerged that some of the people were never interviewed, and that ADTI had not tried to contact Linus Torvalds, or ever put the allegations to him to allow a response. Microsoft attempted to draw a line under this incident, stating that it was a "distraction".

Many suspected that some or all of these legal and fear, uncertainty and doubt (FUD) attacks against the Linux kernel were covertly arranged by Microsoft, although this has never been proven. Both ADTI and SCO, however, received funding from Microsoft.

European Commission v. Microsoft (2004–2007)

In 2004 the European Commission found Microsoft guilty of anti-competitive behaviour with respect to interoperability in the workgroup software market. Microsoft had formerly settled United States v. Microsoft in 2001, in a case which charged that it illegally abused its monopoly power to force computer manufacturers to preinstall Internet Explorer.

The Commission demanded that Microsoft produce full documentation of its workgroup protocols to allow competitors to interoperate with its workgroup software, and imposed fines of 1.5 million euros per day for Microsoft's failure to comply. The commission had jurisdiction because Microsoft sells the software in question in Europe.

Microsoft, after a failed attempt to appeal the decision through the Court of Justice of the European Union, eventually complied with the demand, producing volumes of detailed documentation.

The Samba project, as Microsoft's sole remaining competitor in the workgroup software market, was the key beneficiary of this documentation.

ISO OOXML controversy (2008–present)

In 2008 the International Organization for Standardization published Microsoft's Office Open XML as an international standard, which crucially meant that it, and therefore Microsoft Office, could be used in projects where the use of open standards were mandated by law or by policy. Critics of the standardisation process, including some members of ISO national committees involved in the process itself, alleged irregularities and procedural violations in the process, and argued that the ISO should not have approved OOXML as a standard because it made reference to undocumented Microsoft Office behaviour.

As of 2012, no correct open-source implementation of OOXML exists, which validates the critics' remarks about OOXML being difficult to implement and underspecified. Presently, Google cannot yet convert Office documents into its own proprietary Google Docs format correctly. This suggests that OOXML is not a true open standard, but rather a partial document describing what Microsoft Office does, and only involving certain file formats.

Microsoft's contributions to open source and acquisition of related projects

In 2006 Microsoft launched its CodePlex open source code hosting site, to provide hosting for open-source developers targeting Microsoft platforms. In July 2009 Microsoft even open sourced some Hyper-V-supporting patches to the Linux kernel, because they were required to do so by the GNU General Public License, and contributed them to the mainline kernel. Note that Hyper-V itself is not open source. Microsoft's F# compiler, created in 2002, has also been released as open source under the Apache license. The F# compiler is a commercial product, as it has been incorporated into Microsoft Visual Studio, which is not open source.

Microsoft representatives have made regular appearances at various open source and Linux conferences for many years.

In 2012, Microsoft launched a subsidiary named Microsoft Open Technologies Inc., with the aim of bridging the gap between proprietary Microsoft technologies and non-Microsoft technologies by engaging with open-source standards. This subsidiary was subsequently folded back into Microsoft as Microsoft's position on open source and non-Windows platforms became more favourable.

In January 2016 Microsoft released Chakra as open source under the MIT License; the code is available on GitHub.

Microsoft's stance on open source has shifted as the company began endorsing more open-source software. In 2016, Steve Balmer, former CEO of Microsoft, has retracted his statement that Linux is a malignant cancer. In 2017, the company became a platinum supporter of the Linux Foundation. By 2018, shortly before acquiring GitHub, Microsoft led the charts in the number of paid staff contributing to open-source projects there. While Microsoft may or may not endorse the original philosophy of free software, data shows that it does endorse open source strategically.

Critics have noted that, in March 2019, Microsoft sued Foxconn's subsidiary over a 2013 patent contract; in 2013, Microsoft had announced a patent agreement with Foxconn related to Foxconn's use of the Linux-based Android and ChromeOS.

Open source and programming languages

The vast majority of programming languages in use today have a free software implementation available.

Since the 1990s, the release of major new programming languages in the form of open-source compilers and/or interpreters has been the norm, rather than the exception. Examples include Python in 1991, Ruby in 1995, and Scala in 2003. In recent times, the most notable exceptions have been Java, ActionScript, C#, and Apple's Swift until version 2.2 was proprietary. Partly compatible open-source implementations have been developed for most, and in the case of Java, the main open-source implementation is by now very close to the commercial version.

Java

Since its first public release in 1996, the Java platform had not been open source, although the Java source code portion of the Java runtime was included in Java Development Kits (JDKs), on a purportedly "confidential" basis, despite it being freely downloadable by the general public in most countries. Sun later expanded this "confidential" source code access to include the full source code of the Java Runtime Environment via a separate program which was open to members of the public, and later made the source of the Java compiler javac available also. Sun also made the JDK source code available confidentially to the Blackdown Java project, which was a collection of volunteers who ported early versions of the JDK to Linux, or improved on Sun's Linux ports of the JDK. However, none of this was open source, because modification and redistribution without Sun's permission were forbidden in all cases. Sun stated at the time that they were concerned about preventing forking of the Java platform.

However, several independent partial reimplementations of the Java platform had been created, many of them by the open-source community, such as the GNU Compiler for Java (GCJ). Sun never filed lawsuits against any of the open source clone projects. GCJ notably caused a bad user experience for Java on free software supporting distributions such as Fedora and Ubuntu which shipped GCJ at the time as their Java implementation. How to replace GCJ with the Sun JDK was a frequently asked question by users, because GCJ was an incomplete implementation, incompatible and buggy.

In 2006 Jonathan I. Schwartz became CEO of Sun Microsystems, and signalled his commitment to open source. On 8 May 2007, Sun Microsystems released the Java Development Kit as OpenJDK under the GNU General Public License. Part of the class library (4%) could not be released as open source due to them being licensed from other parties and were included as binary plugs. Because of this, in June 2007, Red Hat launched IcedTea to resolve the encumbered components with the equivalents from GNU Classpath implementation. Since the release, most of the encumbrances have been solved, leaving only the audio engine code and colour management system (the latter is to be resolved using Little CMS).

Distributed version control (2001–present)

The first open-source distributed revision control system (DVCS) was 'tla' in 2001 (since renamed to GNU arch); however, it and its successors 'baz' and 'bzr' (Bazaar) never became very popular, and GNU arch was discontinued, although Bazaar still continues and is used by Canonical.

However, other DVCS projects sprung up, and some started to get significant adoption.

Git (2005–present)

Git, the most popular DVCS, was created in 2005. Some developers of the Linux kernel started to use a proprietary DVCS called BitKeeper, notably Linux founder Linus Torvalds, although some other kernel developers never used it due to its proprietary nature. The unusual situation whereby Linux kernel development involved the use by some of proprietary software "came to a head" when Andrew Tridgell started to reverse-engineer BitKeeper with the aim of producing an open-source tool which could provide some of the same functionality as the commercial version. BitMover, the company that developed BitKeeper, in response, in 2005 revoked the special free of-charge license it had granted to certain kernel developers.

As a result of the removal of the BitKeeper license, Linus Torvalds decided to write his own DVCS, called git, because he thought none of the existing open-source DVCSs were suitable for his particular needs as a kernel maintainer (which was why he had adopted BitKeeper in the first place). A number of other developers quickly jumped in and helped him, and git over time grew from a relatively simple "stupid content tracker" (on which some developers developed "porcelain" extensions) into the sophisticated and powerful DVCS that it is today. Torvalds no longer maintains git himself, however; it has been maintained by Junio Hamano for many years, and has continued receiving contributions from many developers.

The increasing popularity of open-source DVCSs such as git, and then, later, DVCS hosting sites, the most popular of which is GitHub (founded 2008), incrementally reduced the barriers to participation in free software projects still further. With sites like GitHub, no longer did potential contributors have to do things like hunt for the URL for the source code repository (which could be in different places on each website, or sometimes tucked away in a README file or developer documentation), or work out how to generate a patch, and if necessary subscribe to the right mailing list so that their patch email would get to the right people. Contributors can simply fork their own copy of a repository with one click, and issue a pull request from the appropriate branch when their changes are ready. GitHub has become the most popular hosting site in the world for open-source software, and this, together with the ease of forking and the visibility of forks has made it a popular way for contributors to make changes, large and small.

Recent developments

While copyright is the primary legal mechanism that FOSS authors use to ensure license compliance for their software, other mechanisms such as legislation, software patents, and trademarks have uses also. In response to legal issues with patents and the DMCA, the Free Software Foundation released version 3 of its GNU Public License in 2007 that explicitly addressed the DMCA's digital rights management (DRM) provisions and patent rights.

After the development of the GNU GPLv3, as copyright holder of many pieces of the GNU system, such as the GNU Compiler Collection (GCC) software, the FSF updated most of the GNU programs' licenses from GPLv2 to GPLv3. Apple, a user of GCC and a heavy user of both DRM and patents, decided to switch the compiler in its Xcode IDE from GCC to Clang, another FOSS compiler, but which is under a permissive license. LWN speculated that Apple was motivated partly by a desire to avoid GPLv3. The Samba project also switched to GPLv3, which Apple replaced in their software suite with a closed-source, proprietary software alternative.

Recent mergers have affected major open-source software. Sun Microsystems (Sun) acquired MySQL AB, owner of the popular open-source MySQL database, in 2008.

Oracle in turn purchased Sun in January 2010, acquiring their copyrights, patents, and trademarks. This made Oracle the owner of both the most popular proprietary database and the most popular open-source database (MySQL). Oracle's attempts to commercialize the open-source MySQL database have raised concerns in the FOSS community. Partly in response to uncertainty about the future of MySQL, the FOSS community forked the project into new database systems outside of Oracle's control. These include MariaDB, Percona, and Drizzle. All of these have distinct names; they are distinct projects and cannot use the trademarked name MySQL.

Android (2008–present)

In September 2008, Google released the first version of Android, a new smartphone operating system, as open source (some Google applications that are sometimes but not always bundled with Android are not open source). Initially, the operating system was given away for free by Google, and was eagerly adopted by many handset makers; Google later bought Motorola Mobility and produced its own "vanilla" Android phones and tablets, while continuing to allow other manufacturers to use Android. Android is now the world's most popular mobile platform.

Because Android is based on the Linux kernel, this means that Linux is now the dominant kernel on both mobile platforms (via Android), and supercomputers, and a key player in server operating systems too.

Oracle v. Google

In August 2010, Oracle sued Google claiming that its use of Java in Android infringed on Oracle's copyrights and patents. The initial Oracle v. Google trial ended in May 2012, with the finding that Google did not infringe on Oracle's patents, and the trial judge ruled that the structure of the Java application programming interfaces (APIs) used by Google was not copyrightable. The jury found that Google made a trivial ("de minimis") copyright infringement, but the parties stipulated that Google would pay no damages, because it was so trivial. However, Oracle appealed to the Federal Circuit, and Google filed a cross-appeal on the literal copying claim. The Federal Circuit ruled that the small copyright infringement acknowledged by Google was not de minimis, and sent the fair use issue back to the trial judge for reconsideration. In 2016, the case was retried and a jury found for Google, on the grounds of fair use.

Chromium OS (2009–present)

Until recently, Linux was still a relatively uncommon choice of operating system for desktops and laptops. However, Google's Chromebooks, running ChromeOS which is essentially a thin client, have captured 20–25% of the sub-$300 US laptop market. ChromeOS is built from the open-source ChromiumOS, which is based on Linux, in much the same way that versions of Android shipped on commercially available phones are built from the open source version of Android.

Cytoskeleton

From Wikipedia, the free encyclopedia
 
Cell biology
Animal cell diagram
The cytoskeleton consists of (a) microtubules, (b) microfilaments, and (c) intermediate filaments.

The cytoskeleton is a complex, dynamic network of interlinking protein filaments present in the cytoplasm of all cells, including those of bacteria and archaea. In eukaryotes, it extends from the cell nucleus to the cell membrane and is composed of similar proteins in the various organisms. It is composed of three main components, microfilaments, intermediate filaments and microtubules, and these are all capable of rapid growth or disassembly dependent on the cell's requirements.

A multitude of functions can be performed by the cytoskeleton. Its primary function is to give the cell its shape and mechanical resistance to deformation, and through association with extracellular connective tissue and other cells it stabilizes entire tissues. The cytoskeleton can also contract, thereby deforming the cell and the cell's environment and allowing cells to migrate. Moreover, it is involved in many cell signaling pathways and in the uptake of extracellular material (endocytosis), the segregation of chromosomes during cellular division, the cytokinesis stage of cell division, as scaffolding to organize the contents of the cell in space and in intracellular transport (for example, the movement of vesicles and organelles within the cell) and can be a template for the construction of a cell wall. Furthermore, it can form specialized structures, such as flagella, cilia, lamellipodia and podosomes. The structure, function and dynamic behavior of the cytoskeleton can be very different, depending on organism and cell type. Even within one cell, the cytoskeleton can change through association with other proteins and the previous history of the network.

A large-scale example of an action performed by the cytoskeleton is muscle contraction. This is carried out by groups of highly specialized cells working together. A main component in the cytoskeleton that helps show the true function of this muscle contraction is the microfilament. Microfilaments are composed of the most abundant cellular protein known as actin. During contraction of a muscle, within each muscle cell, myosin molecular motors collectively exert forces on parallel actin filaments. Muscle contraction starts from nerve impulses which then causes increased amounts of calcium to be released from the sarcoplasmic reticulum. Increases in calcium in the cytosol allows muscle contraction to begin with the help of two proteins, tropomyosin and troponin. Tropomyosin inhibits the interaction between actin and myosin, while troponin senses the increase in calcium and releases the inhibition. This action contracts the muscle cell, and through the synchronous process in many muscle cells, the entire muscle.

History

In 1903, Nikolai K. Koltsov proposed that the shape of cells was determined by a network of tubules that he termed the cytoskeleton. The concept of a protein mosaic that dynamically coordinated cytoplasmic biochemistry was proposed by Rudolph Peters in 1929 while the term (cytosquelette, in French) was first introduced by French embryologist Paul Wintrebert in 1931.

When the cytoskeleton was first introduced, it was thought to be an uninteresting gel-like substance that helped organelles stay in place. Much research took place to try to understand the purpose of the cytoskeleton and its components.

Initially, it was thought that the cytoskeleton was exclusive to eukaryotes but in 1992 it was discovered to be present in prokaryotes as well. This discovery came after the realization that bacteria possess proteins that are homologous to tubulin and actin; the main components of the eukaryotic cytoskeleton.

Eukaryotic cytoskeleton

Eukaryotic cells contain three main kinds of cytoskeletal filaments: microfilaments, microtubules, and intermediate filaments. In neurons the intermediate filaments are known as neurofilaments. Each type is formed by the polymerization of a distinct type of protein subunit and has its own characteristic shape and intracellular distribution. Microfilaments are polymers of the protein actin and are 7 nm in diameter. Microtubules are composed of tubulin and are 25 nm in diameter. Intermediate filaments are composed of various proteins, depending on the type of cell in which they are found; they are normally 8-12 nm in diameter. The cytoskeleton provides the cell with structure and shape, and by excluding macromolecules from some of the cytosol, it adds to the level of macromolecular crowding in this compartment. Cytoskeletal elements interact extensively and intimately with cellular membranes.

Research into neurodegenerative disorders such as Parkinson's disease, Alzheimer's disease, Huntington's disease, and amyotrophic lateral sclerosis (ALS) indicate that the cytoskeleton is affected in these diseases. Parkinson's disease is marked by the degradation of neurons, resulting in tremors, rigidity, and other non-motor symptoms. Research has shown that microtubule assembly and stability in the cytoskeleton is compromised causing the neurons to degrade over time. In Alzheimer's disease, tau proteins which stabilize microtubules malfunction in the progression of the illness causing pathology of the cytoskeleton. Excess glutamine in the Huntington protein involved with linking vesicles onto the cytoskeleton is also proposed to be a factor in the development of Huntington's Disease. Amyotrophic lateral sclerosis results in a loss of movement caused by the degradation of motor neurons, and also involves defects of the cytoskeleton.

Stuart Hameroff and Roger Penrose suggest a role of microtubule vibrations in neurons in the origin of consciousness.

Accessory proteins including motor proteins regulate and link the filaments to other cell compounds and each other and are essential for controlled assembly of cytoskeletal filaments in particular locations.

A number of small-molecule cytoskeletal drugs have been discovered that interact with actin and microtubules. These compounds have proven useful in studying the cytoskeleton, and several have clinical applications.

Microfilaments

Structure of a microfilament
 
Actin cytoskeleton of mouse embryo fibroblasts, stained with phalloidin

Microfilaments, also known as actin filaments, are composed of linear polymers of G-actin proteins, and generate force when the growing (plus) end of the filament pushes against a barrier, such as the cell membrane. They also act as tracks for the movement of myosin molecules that affix to the microfilament and "walk" along them. In general, the major component or protein of microfilaments are actin. The G-actin monomer combines to form a polymer which continues to form the microfilament (actin filament). These subunits then assemble into two chains that intertwine into what are called F-actin chains. Myosin motoring along F-actin filaments generates contractile forces in so-called actomyosin fibers, both in muscle as well as most non-muscle cell types. Actin structures are controlled by the Rho family of small GTP-binding proteins such as Rho itself for contractile acto-myosin filaments ("stress fibers"), Rac for lamellipodia and Cdc42 for filopodia.

Functions include:

Intermediate filaments

Structure of an intermediate filament
 
Microscopy of keratin filaments inside cells

Intermediate filaments are a part of the cytoskeleton of many eukaryotic cells. These filaments, averaging 10 nanometers in diameter, are more stable (strongly bound) than microfilaments, and heterogeneous constituents of the cytoskeleton. Like actin filaments, they function in the maintenance of cell-shape by bearing tension (microtubules, by contrast, resist compression but can also bear tension during mitosis and during the positioning of the centrosome). Intermediate filaments organize the internal tridimensional structure of the cell, anchoring organelles and serving as structural components of the nuclear lamina. They also participate in some cell-cell and cell-matrix junctions. Nuclear lamina exist in all animals and all tissues. Some animals like the fruit fly do not have any cytoplasmic intermediate filaments. In those animals that express cytoplasmic intermediate filaments, these are tissue specific. Keratin intermediate filaments in epithelial cells provide protection for different mechanical stresses the skin may endure. They also provide protection for organs against metabolic, oxidative, and chemical stresses. Strengthening of epithelial cells with these intermediate filaments may prevent onset of apoptosis, or cell death, by reducing the probability of stress.

Intermediate filaments are most commonly known as the support system or "scaffolding" for the cell and nucleus while also playing a role in some cell functions. In combination with proteins and desmosomes, the intermediate filaments form cell-cell connections and anchor the cell-matrix junctions that are used in messaging between cells as well as vital functions of the cell. These connections allow the cell to communicate through the desmosome of multiple cells to adjust structures of the tissue based on signals from the cells environment. Mutations in the IF proteins have been shown to cause serious medical issues such as premature aging, desmin mutations compromising organs, Alexander Disease, and muscular dystrophy.

Different intermediate filaments are:

  • made of vimentins. Vimentin intermediate filaments are in general present in mesenchymal cells.
  • made of keratin. Keratin is present in general in epithelial cells.
  • neurofilaments of neural cells.
  • made of lamin, giving structural support to the nuclear envelope.
  • made of desmin, play an important role in structural and mechanical support of muscle cells.

Microtubules

Structure of a microtubule
 
Microtubules in a gel-fixated cell

Microtubules are hollow cylinders about 23 nm in diameter (lumen diameter of approximately 15 nm), most commonly comprising 13 protofilaments that, in turn, are polymers of alpha and beta tubulin. They have a very dynamic behavior, binding GTP for polymerization. They are commonly organized by the centrosome.

In nine triplet sets (star-shaped), they form the centrioles, and in nine doublets oriented about two additional microtubules (wheel-shaped), they form cilia and flagella. The latter formation is commonly referred to as a "9+2" arrangement, wherein each doublet is connected to another by the protein dynein. As both flagella and cilia are structural components of the cell, and are maintained by microtubules, they can be considered part of the cytoskeleton. There are two types of cilia: motile and non-motile cilia. Cilia are short and more numerous than flagella. The motile cilia have a rhythmic waving or beating motion compared to the non-motile cilia which receive sensory information for the cell; processing signals from the other cells or the fluids surrounding it. Additionally, the microtubules control the beating (movement) of the cilia and flagella. Also, the dynein arms attached to the microtubules function as the molecular motors. The motion of the cilia and flagella is created by the microtubules sliding past one another, which requires ATP. They play key roles in:

In addition to the roles described above, Stuart Hameroff and Roger Penrose have proposed that microtubules function in consciousness.

Comparison

Cytoskeleton
type
Diameter
(nm)
Structure Subunit examples
Microfilaments 6 Double helix Actin
Intermediate
filaments
10 Two anti-parallel helices/dimers, forming tetramers
Microtubules 23 Protofilaments, in turn consisting of tubulin subunits in complex with stathmin α- and β-Tubulin

Septins

Septins are a group of the highly conserved GTP binding proteins found in eukaryotes. Different septins form protein complexes with each other. These can assemble to filaments and rings. Therefore, septins can be considered part of the cytoskeleton. The function of septins in cells include serving as a localized attachment site for other proteins, and preventing the diffusion of certain molecules from one cell compartment to another. In yeast cells, they build scaffolding to provide structural support during cell division and compartmentalize parts of the cell. Recent research in human cells suggests that septins build cages around bacterial pathogens, immobilizing the harmful microbes and preventing them from invading other cells.

Spectrin

Spectrin is a cytoskeletal protein that lines the intracellular side of the plasma membrane in eukaryotic cells. Spectrin forms pentagonal or hexagonal arrangements, forming a scaffolding and playing an important role in maintenance of plasma membrane integrity and cytoskeletal structure.

Yeast cytoskeleton

In budding yeast (an important model organism), actin forms cortical patches, actin cables, and a cytokinetic ring and the cap. Cortical patches are discrete actin bodies on the membrane and are vital for endocytosis, especially the recycling of glucan synthase which is important for cell wall synthesis. Actin cables are bundles of actin filaments and are involved in the transport of vesicles towards the cap (which contains a number of different proteins to polarize cell growth) and in the positioning of mitochondria. The cytokinetic ring forms and constricts around the site of cell division.

Prokaryotic cytoskeleton

Prior to the work of Jones et al., 2001, the cell wall was believed to be the deciding factor for many bacterial cell shapes, including rods and spirals. When studied, many misshapen bacteria were found to have mutations linked to development of a cell envelope. The cytoskeleton was once thought to be a feature only of eukaryotic cells, but homologues to all the major proteins of the eukaryotic cytoskeleton have been found in prokaryotes. Harold Erickson notes that before 1992, only eukaryotes were believed to have cytoskeleton components. However, research in the early '90s suggested that bacteria and archaea had homologues of actin and tubulin, and that these were the basis of eukaryotic microtubules and microfilaments. Although the evolutionary relationships are so distant that they are not obvious from protein sequence comparisons alone, the similarity of their three-dimensional structures and similar functions in maintaining cell shape and polarity provides strong evidence that the eukaryotic and prokaryotic cytoskeletons are truly homologous. Three laboratories independently discovered that FtsZ, a protein already known as a key player in bacterial cytokinesis, had the "tubulin signature sequence" present in all α-, β-, and γ-tubulins. However, some structures in the bacterial cytoskeleton may not have been identified as of yet.

FtsZ

FtsZ was the first protein of the prokaryotic cytoskeleton to be identified. Like tubulin, FtsZ forms filaments in the presence of guanosine triphosphate (GTP), but these filaments do not group into tubules. During cell division, FtsZ is the first protein to move to the division site, and is essential for recruiting other proteins that synthesize the new cell wall between the dividing cells.

MreB and ParM

Prokaryotic actin-like proteins, such as MreB, are involved in the maintenance of cell shape. All non-spherical bacteria have genes encoding actin-like proteins, and these proteins form a helical network beneath the cell membrane that guides the proteins involved in cell wall biosynthesis.

Some plasmids encode a separate system that involves an actin-like protein ParM. Filaments of ParM exhibit dynamic instability, and may partition plasmid DNA into the dividing daughter cells by a mechanism analogous to that used by microtubules during eukaryotic mitosis.

Crescentin

The bacterium Caulobacter crescentus contains a third protein, crescentin, that is related to the intermediate filaments of eukaryotic cells. Crescentin is also involved in maintaining cell shape, such as helical and vibrioid forms of bacteria, but the mechanism by which it does this is currently unclear. Additionally, curvature could be described by the displacement of crescentic filaments, after the disruption of peptidoglycan synthesis.

The cytoskeleton and cell mechanics

The cytoskeleton is a highly anisotropic and dynamic network, constantly remodeling itself in response to the changing cellular microenvironment. The network influences cell mechanics and dynamics by differentially polymerizing and depolymerizing its constituent filaments (primarily actin and myosin, but microtubules and intermediate filaments also play a role). This generates forces, which play an important role in informing the cell of its microenvironment. Specifically, forces such as tension, stiffness, and shear forces have all been shown to influence cell fate, differentiation, migration, and motility. Through a process called “mechanotransduction,” the cell remodels its cytoskeleton to sense and respond to these forces.

Mechanotransduction relies heavily on focal adhesions, which essentially connect the intracellular cytoskeleton with the extracellular matrix (ECM). Through focal adhesions, the cell is able to integrate extracellular forces into intracellular ones as the proteins present at focal adhesions undergo conformational changes to initiate signaling cascades. Proteins such as focal adhesion kinase (FAK) and Src have been shown to transduce force signals in response to cellular activities such as proliferation and differentiation, and are hypothesized to be key sensors in the mechanotransduction pathway. As a result of mechanotransduction, the cytoskeleton changes its composition and/or orientation to accommodate the force stimulus and ensure the cell responds accordingly.

The cytoskeleton changes the mechanics of the cell in response to detected forces. For example, increasing tension within the plasma membrane makes it more likely that ion channels will open, which increases ion conductance and makes cellular change ion influx or efflux much more likely. Moreover, the mechanical properties of cells determine how far and where, directionally, a force will propagate throughout the cell and how it will change cell dynamics. A membrane protein that is not closely coupled to the cytoskeleton, for instance, will not produce a significant effect on the cortical actin network if it is subjected to a specifically directed force. However, membrane proteins that are more closely associated with the cytoskeleton will induce a more significant response. In this way, the anisotropy of the cytoskeleton serves to more keenly direct cell responses to intra or extracellular signals.

Long-range order

The specific pathways and mechanisms by which the cytoskeleton senses and responds to forces are still under investigation. However, the long-range order generated by the cytoskeleton is known to contribute to mechanotransduction. Cells, which are around 10–50 μm in diameter, are several thousand times larger than the molecules found within the cytoplasm that are essential to coordinate cellular activities. Because cells are so large in comparison to essential biomolecules, it is difficult, in the absence of an organizing network, for different parts of the cytoplasm to communicate. Moreover, biomolecules must polymerize to lengths comparable to the length of the cell, but resulting polymers can be highly disorganized and unable to effectively transmit signals from one part of the cytoplasm to another. Thus, it is necessary to have the cytoskeleton to organize the polymers and ensure that they can effectively communicate across the entirety of the cell.

Common features and differences between prokaryotes and eukaryotes

By definition, the cytoskeleton is composed of proteins that can form longitudinal arrays (fibres) in all organisms. These filament forming proteins have been classified into 4 classes. Tubulin-like, actin-like, Walker A cytoskeletal ATPases (WACA-proteins), and intermediate filaments.

Tubulin-like proteins are tubulin in eukaryotes and FtsZ, TubZ, RepX in prokaryotes. Actin-like proteins are actin in eukaryotes and MreB, FtsA in prokaryotes. An example of a WACA-proteins, which are mostly found in prokaryotes, is MinD. Examples for intermediate filaments, which have almost exclusively been found in animals (i.e. eukaryotes) are the lamins, keratins, vimentin, neurofilaments, and desmin.

Although tubulin-like proteins share some amino acid sequence similarity, their equivalence in protein-fold and the similarity in the GTP binding site is more striking. The same holds true for the actin-like proteins and their structure and ATP binding domain.

Cytoskeletal proteins are usually correlated with cell shape, DNA segregation and cell division in prokaryotes and eukaryotes. Which proteins fulfill which task is very different. For example, DNA segregation in all eukaryotes happens through use of tubulin, but in prokaryotes either WACA proteins, actin-like or tubulin-like proteins can be used. Cell division is mediated in eukaryotes by actin, but in prokaryotes usually by tubulin-like (often FtsZ-ring) proteins and sometimes (Thermoproteota) ESCRT-III, which in eukaryotes still has a role in the last step of division.

Cytoplasmic streaming

Cytoplasmic streaming, also known as cyclosis, is the active movement of a cell’s contents along the components of the cytoskeleton. While mainly seen in plants, all cell types use this process for transportation of waste, nutrients, and organelles to other parts of the cell.  Plant and algae cells are generally larger than many other cells; so cytoplasmic streaming is important in these types of cells. This is because the cell’s extra volume requires cytoplasmic streaming in order to move organelles throughout the entire cell. Organelles move along microfilaments in the cytoskeleton driven by myosin motors binding and pushing along actin filament bundles.

Herbivore

From Wikipedia, the free encyclopedia
A deer and two fawns feeding on foliage
A sawfly larva feeding on a leaf
Tracks made by terrestrial gastropods with their radulas, scraping green algae from a surface inside a greenhouse

A herbivore is an animal anatomically and physiologically adapted to eating plant material, for example foliage or marine algae, for the main component of its diet. As a result of their plant diet, herbivorous animals typically have mouthparts adapted to rasping or grinding. Horses and other herbivores have wide flat teeth that are adapted to grinding grass, tree bark, and other tough plant material.

A large percentage of herbivores have mutualistic gut flora that help them digest plant matter, which is more difficult to digest than animal prey. This flora is made up of cellulose-digesting protozoans or bacteria.

Etymology

Herbivore is the anglicized form of a modern Latin coinage, herbivora, cited in Charles Lyell's 1830 Principles of Geology. Richard Owen employed the anglicized term in an 1854 work on fossil teeth and skeletons. Herbivora is derived from Latin herba 'small plant, herb' and vora, from vorare 'to eat, devour'.

Definition and related terms

Herbivory is a form of consumption in which an organism principally eats autotrophs such as plants, algae and photosynthesizing bacteria. More generally, organisms that feed on autotrophs in general are known as primary consumers. Herbivory is usually limited to animals that eat plants. Insect herbivory can cause a variety of physical and metabolic alterations in the way the host plant interacts with itself and other surrounding biotic factors. Fungi, bacteria, and protists that feed on living plants are usually termed plant pathogens (plant diseases), while fungi and microbes that feed on dead plants are described as saprotrophs. Flowering plants that obtain nutrition from other living plants are usually termed parasitic plants. There is, however, no single exclusive and definitive ecological classification of consumption patterns; each textbook has its own variations on the theme.

Evolution of herbivory

A fossil Viburnum lesquereuxii leaf with evidence of insect herbivory; Dakota Sandstone (Cretaceous) of Ellsworth County, Kansas. Scale bar is 10 mm.

The understanding of herbivory in geological time comes from three sources: fossilized plants, which may preserve evidence of defence (such as spines), or herbivory-related damage; the observation of plant debris in fossilised animal faeces; and the construction of herbivore mouthparts.

Although herbivory was long thought to be a Mesozoic phenomenon, fossils have shown that plants were being consumed by arthropods within less than 20 million years after the first land plants evolved. Insects fed on the spores of early Devonian plants, and the Rhynie chert also provides evidence that organisms fed on plants using a "pierce and suck" technique.

During the next 75 million years, plants evolved a range of more complex organs, such as roots and seeds. There is no evidence of any organism being fed upon until the middle-late Mississippian, 330.9 million years ago. There was a gap of 50 to 100 million years between the time each organ evolved and the time organisms evolved to feed upon them; this may be due to the low levels of oxygen during this period, which may have suppressed evolution. Further than their arthropod status, the identity of these early herbivores is uncertain. Hole feeding and skeletonization are recorded in the early Permian, with surface fluid feeding evolving by the end of that period.

Herbivory among four-limbed terrestrial vertebrates, the tetrapods, developed in the Late Carboniferous (307–299 million years ago). Early tetrapods were large amphibious piscivores. While amphibians continued to feed on fish and insects, some reptiles began exploring two new food types, tetrapods (carnivory) and plants (herbivory). The entire dinosaur order ornithischia was composed of herbivorous dinosaurs. Carnivory was a natural transition from insectivory for medium and large tetrapods, requiring minimal adaptation. In contrast, a complex set of adaptations was necessary for feeding on highly fibrous plant materials.

Arthropods evolved herbivory in four phases, changing their approach to it in response to changing plant communities.Tetrapod herbivores made their first appearance in the fossil record of their jaws near the Permio-Carboniferous boundary, approximately 300 million years ago. The earliest evidence of their herbivory has been attributed to dental occlusion, the process in which teeth from the upper jaw come in contact with teeth in the lower jaw is present. The evolution of dental occlusion led to a drastic increase in plant food processing and provides evidence about feeding strategies based on tooth wear patterns. Examination of phylogenetic frameworks of tooth and jaw morphologes has revealed that dental occlusion developed independently in several lineages tetrapod herbivores. This suggests that evolution and spread occurred simultaneously within various lineages.

Food chain

Leaf miners feed on leaf tissue between the epidermal layers, leaving visible trails

Herbivores form an important link in the food chain because they consume plants to digest the carbohydrates photosynthetically produced by a plant. Carnivores in turn consume herbivores for the same reason, while omnivores can obtain their nutrients from either plants or animals. Due to a herbivore's ability to survive solely on tough and fibrous plant matter, they are termed the primary consumers in the food cycle (chain). Herbivory, carnivory, and omnivory can be regarded as special cases of consumer–resource interactions.

Feeding strategies

Two herbivore feeding strategies are grazing (e.g. cows) and browsing (e.g. moose). For a terrestrial mammal to be called a grazer, at least 90% of the forage has to be grass, and for a browser at least 90% tree leaves and twigs. An intermediate feeding strategy is called "mixed-feeding". In their daily need to take up energy from forage, herbivores of different body mass may be selective in choosing their food. "Selective" means that herbivores may choose their forage source depending on, e.g., season or food availability, but also that they may choose high quality (and consequently highly nutritious) forage before lower quality. The latter especially is determined by the body mass of the herbivore, with small herbivores selecting for high-quality forage, and with increasing body mass animals are less selective. Several theories attempt to explain and quantify the relationship between animals and their food, such as Kleiber's law, Holling's disk equation and the marginal value theorem (see below).

Kleiber's law describes the relationship between an animal's size and its feeding strategy, saying that larger animals need to eat less food per unit weight than smaller animals. Kleiber's law states that the metabolic rate (q0) of an animal is the mass of the animal (M) raised to the 3/4 power: q0=M3/4 Therefore, the mass of the animal increases at a faster rate than the metabolic rate.

Herbivores employ numerous types of feeding strategies. Many herbivores do not fall into one specific feeding strategy, but employ several strategies and eat a variety of plant parts.

Types of feeding strategies
Feeding Strategy Diet Examples
Algivores Algae Krill, crabs, sea snail, sea urchin, parrotfish, surgeonfish, flamingo
Frugivores Fruit Ruffed lemurs, orangutans
Folivores Leaves Koalas, gorillas, red colobuses, many leaf beetles
Nectarivores Nectar Honey possums, hummingbirds
Granivores Seeds Hawaiian honeycreepers, bean weevils
Graminivores Grass Horses
Palynivores Pollen Bees
Mucivores Plant fluids, i.e. sap Aphids
Xylophages Wood Termites, longicorn beetles, ambrosia beetles

Optimal foraging theory is a model for predicting animal behavior while looking for food or other resources, such as shelter or water. This model assesses both individual movement, such as animal behavior while looking for food, and distribution within a habitat, such as dynamics at the population and community level. For example, the model would be used to look at the browsing behavior of a deer while looking for food, as well as that deer's specific location and movement within the forested habitat and its interaction with other deer while in that habitat.

This model has been criticized as circular and untestable. Critics have pointed out that its proponents use examples that fit the theory, but do not use the model when it does not fit the reality. Other critics point out that animals do not have the ability to assess and maximize their potential gains, therefore the optimal foraging theory is irrelevant and derived to explain trends that do not exist in nature.

Holling's disk equation models the efficiency at which predators consume prey. The model predicts that as the number of prey increases, the amount of time predators spend handling prey also increases, and therefore the efficiency of the predator decreases. In 1959, S. Holling proposed an equation to model the rate of return for an optimal diet: Rate (R )=Energy gained in foraging (Ef)/(time searching (Ts) + time handling (Th))

Where s=cost of search per unit time f=rate of encounter with items, h=handling time, e=energy gained per encounter
In effect, this would indicate that a herbivore in a dense forest would spend more time handling (eating) the vegetation because there was so much vegetation around than a herbivore in a sparse forest, who could easily browse through the forest vegetation. According to the Holling's disk equation, a herbivore in the sparse forest would be more efficient at eating than the herbivore in the dense forest.

The marginal value theorem describes the balance between eating all the food in a patch for immediate energy, or moving to a new patch and leaving the plants in the first patch to regenerate for future use. The theory predicts that absent complicating factors, an animal should leave a resource patch when the rate of payoff (amount of food) falls below the average rate of payoff for the entire area. According to this theory, an animal should move to a new patch of food when the patch they are currently feeding on requires more energy to obtain food than an average patch. Within this theory, two subsequent parameters emerge, the Giving Up Density (GUD) and the Giving Up Time (GUT). The Giving Up Density (GUD) quantifies the amount of food that remains in a patch when a forager moves to a new patch. The Giving Up Time (GUT) is used when an animal continuously assesses the patch quality.

Plant-herbivore interactions

Interactions between plants and herbivores can play a prevalent role in ecosystem dynamics such community structure and functional processes. Plant diversity and distribution is often driven by herbivory, and it is likely that trade-offs between plant competitiveness and defensiveness, and between colonization and mortality allow for coexistence between species in the presence of herbivores. However, the effects of herbivory on plant diversity and richness is variable. For example, increased abundance of herbivores such as deer decrease plant diversity and species richness, while other large mammalian herbivores like bison control dominant species which allows other species to flourish. Plant-herbivore interactions can also operate so that plant communities mediate herbivore communities. Plant communities that are more diverse typically sustain greater herbivore richness by providing a greater and more diverse set of resources.

Coevolution and phylogenetic correlation between herbivores and plants are important aspects of the influence of herbivore and plant interactions on communities and ecosystem functioning, especially in regard to herbivorous insects. This is apparent in the adaptations plants develop to tolerate and/or defend from insect herbivory and the responses of herbivores to overcome these adaptations. The evolution of antagonistic and mutualistic plant-herbivore interactions are not mutually exclusive and may co-occur. Plant phylogeny has been found to facilitate the colonization and community assembly of herbivores, and there is evidence of phylogenetic linkage between plant beta diversity and phylogenetic beta diversity of insect clades such as butterflies. These types of eco-evolutionary feedbacks between plants and herbivores are likely the main driving force behind plant and herbivore diversity.

Abiotic factors such as climate and biogeographical features also impact plant-herbivore communities and interactions. For example, in temperate freshwater wetlands herbivorous waterfowl communities change according to season, with species that eat above-ground vegetation being abundant during summer, and species that forage below-ground being present in winter months. These seasonal herbivore communities differ in both their assemblage and functions within the wetland ecosystem. Such differences in herbivore modalities can potentially lead to trade-offs that influence species traits and may lead to additive effects on community composition and ecosystem functioning. Seasonal changes and environmental gradients such as elevation and latitude often affect the palatability of plants which in turn influences herbivore community assemblages and vice versa. Examples include a decrease in abundance of leaf-chewing larvae in the fall when hardwood leaf palatability decreases due to increased tannin levels which results in a decline of arthropod species richness, and increased palatability of plant communities at higher elevations where grasshoppers abundances are lower. Climatic stressors such as ocean acidification can lead to responses in plant-herbivore interactions in relation to palatability as well.

Herbivore offense

Aphids are fluid feeders on plant sap.

The myriad defenses displayed by plants means that their herbivores need a variety of skills to overcome these defenses and obtain food. These allow herbivores to increase their feeding and use of a host plant. Herbivores have three primary strategies for dealing with plant defenses: choice, herbivore modification, and plant modification.

Feeding choice involves which plants a herbivore chooses to consume. It has been suggested that many herbivores feed on a variety of plants to balance their nutrient uptake and to avoid consuming too much of any one type of defensive chemical. This involves a tradeoff however, between foraging on many plant species to avoid toxins or specializing on one type of plant that can be detoxified.

Herbivore modification is when various adaptations to body or digestive systems of the herbivore allow them to overcome plant defenses. This might include detoxifying secondary metabolites, sequestering toxins unaltered, or avoiding toxins, such as through the production of large amounts of saliva to reduce effectiveness of defenses. Herbivores may also utilize symbionts to evade plant defenses. For example, some aphids use bacteria in their gut to provide essential amino acids lacking in their sap diet.

Plant modification occurs when herbivores manipulate their plant prey to increase feeding. For example, some caterpillars roll leaves to reduce the effectiveness of plant defenses activated by sunlight.

Plant defense

A plant defense is a trait that increases plant fitness when faced with herbivory. This is measured relative to another plant that lacks the defensive trait. Plant defenses increase survival and/or reproduction (fitness) of plants under pressure of predation from herbivores.

Defense can be divided into two main categories, tolerance and resistance. Tolerance is the ability of a plant to withstand damage without a reduction in fitness. This can occur by diverting herbivory to non-essential plant parts, resource allocation, compensatory growth, or by rapid regrowth and recovery from herbivory. Resistance refers to the ability of a plant to reduce the amount of damage it receives from herbivores. This can occur via avoidance in space or time, physical defenses, or chemical defenses. Defenses can either be constitutive, always present in the plant, or induced, produced or translocated by the plant following damage or stress.

Physical, or mechanical, defenses are barriers or structures designed to deter herbivores or reduce intake rates, lowering overall herbivory. Thorns such as those found on roses or acacia trees are one example, as are the spines on a cactus. Smaller hairs known as trichomes may cover leaves or stems and are especially effective against invertebrate herbivores. In addition, some plants have waxes or resins that alter their texture, making them difficult to eat. Also the incorporation of silica into cell walls is analogous to that of the role of lignin in that it is a compression-resistant structural component of cell walls; so that plants with their cell walls impregnated with silica are thereby afforded a measure of protection against herbivory.

Chemical defenses are secondary metabolites produced by the plant that deter herbivory. There are a wide variety of these in nature and a single plant can have hundreds of different chemical defenses. Chemical defenses can be divided into two main groups, carbon-based defenses and nitrogen-based defenses.

  1. Carbon-based defenses include terpenes and phenolics. Terpenes are derived from 5-carbon isoprene units and comprise essential oils, carotenoids, resins, and latex. They can have several functions that disrupt herbivores such as inhibiting adenosine triphosphate (ATP) formation, molting hormones, or the nervous system. Phenolics combine an aromatic carbon ring with a hydroxyl group. There are several different phenolics such as lignins, which are found in cell walls and are very indigestible except for specialized microorganisms; tannins, which have a bitter taste and bind to proteins making them indigestible; and furanocumerins, which produce free radicals disrupting DNA, protein, and lipids, and can cause skin irritation.
  2. Nitrogen-based defenses are synthesized from amino acids and primarily come in the form of alkaloids and cyanogens. Alkaloids include commonly recognized substances such as caffeine, nicotine, and morphine. These compounds are often bitter and can inhibit DNA or RNA synthesis or block nervous system signal transmission. Cyanogens get their name from the cyanide stored within their tissues. This is released when the plant is damaged and inhibits cellular respiration and electron transport.

Plants have also changed features that enhance the probability of attracting natural enemies to herbivores. Some emit semiochemicals, odors that attract natural enemies, while others provide food and housing to maintain the natural enemies' presence, e.g. ants that reduce herbivory. A given plant species often has many types of defensive mechanisms, mechanical or chemical, constitutive or induced, which allow it to escape from herbivores.

Predator–prey theory

According to the theory of predator–prey interactions, the relationship between herbivores and plants is cyclic. When prey (plants) are numerous their predators (herbivores) increase in numbers, reducing the prey population, which in turn causes predator number to decline. The prey population eventually recovers, starting a new cycle. This suggests that the population of the herbivore fluctuates around the carrying capacity of the food source, in this case, the plant.

Several factors play into these fluctuating populations and help stabilize predator-prey dynamics. For example, spatial heterogeneity is maintained, which means there will always be pockets of plants not found by herbivores. This stabilizing dynamic plays an especially important role for specialist herbivores that feed on one species of plant and prevents these specialists from wiping out their food source. Prey defenses also help stabilize predator-prey dynamics, and for more information on these relationships see the section on Plant Defenses. Eating a second prey type helps herbivores' populations stabilize. Alternating between two or more plant types provides population stability for the herbivore, while the populations of the plants oscillate. This plays an important role for generalist herbivores that eat a variety of plants. Keystone herbivores keep vegetation populations in check and allow for a greater diversity of both herbivores and plants. When an invasive herbivore or plant enters the system, the balance is thrown off and the diversity can collapse to a monotaxon system.

The back and forth relationship of plant defense and herbivore offense drives coevolution between plants and herbivores, resulting in a "coevolutionary arms race". The escape and radiation mechanisms for coevolution, presents the idea that adaptations in herbivores and their host plants, has been the driving force behind speciation.

Mutualism

While much of the interaction of herbivory and plant defense is negative, with one individual reducing the fitness of the other, some is beneficial. This beneficial herbivory takes the form of mutualisms in which both partners benefit in some way from the interaction. Seed dispersal by herbivores and pollination are two forms of mutualistic herbivory in which the herbivore receives a food resource and the plant is aided in reproduction. Plants can also be indirectly affected by herbivores through nutrient recycling, with plants benefiting from herbivores when nutrients are recycled very efficiently. Another form of plant-herbivore mutualism is physical changes to the environment and/or plant community structure by herbivores which serve as ecosystem engineers, such as wallowing by bison. Swans form a mutual relationship with the plant species that they forage by digging and disturbing the sediment which removes competing plants and subsequently allows colonization of other plant species.

Impacts

Mixed feeding shoal of herbivorous fish on a coral reef

Trophic cascades and environmental degradation

When herbivores are affected by trophic cascades, plant communities can be indirectly affected. Often these effects are felt when predator populations decline and herbivore populations are no longer limited, which leads to intense herbivore foraging which can suppress plant communities. With the size of herbivores having an effect on the amount of energy intake that is needed, larger herbivores need to forage on higher quality or more plants to gain the optimal amount of nutrients and energy compared to smaller herbivores. Environmental degradation from white-tailed deer (Odocoileus virginianus) in the US alone has the potential to both change vegetative communities through over-browsing and cost forest restoration projects upwards of $750 million annually. Another example of a trophic cascade involved plant-herbivore interactions are coral reef ecosystems. Herbivorous fish and marine animals are important algae and seaweed grazers, and in the absence of plant-eating fish, corals are outcompeted and seaweeds deprive corals of sunlight.

Economic impacts

Agricultural crop damage by the same species totals approximately $100 million every year. Insect crop damages also contribute largely to annual crop losses in the U.S. Herbivores also affect economics through the revenue generated by hunting and ecotourism. For example, the hunting of herbivorous game species such as white-tailed deer, cottontail rabbits, antelope, and elk in the U.S. contributes greatly to the billion-dollar annually, hunting industry. Ecotourism is a major source of revenue, particularly in Africa, where many large mammalian herbivores such as elephants, zebras, and giraffes help to bring in the equivalent of millions of US dollars to various nations annually.

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