Putting A Face On Machine Mutation - 4

First Came the Machines

One statement gets our attention anytime we talk about machine mutation and/or machine evolution.

That statement is: DNA is not alive, is not life, it is a molecule, it is not living - it is a molecular machine.

Add to that peculiarity the narrative pointed out in this series, a narrative not always considered in discussions concerning evolution, which is that machine evolution has taken up the vast majority of evolutionary dynamics, especially in terms of the percentage of the span of the evolutionary timescale (Putting A Face On Machine Mutation - 3).

Thus, we come to the focus of today's post, which is the observation that one of the candidates for the apex of machine evolution, reached during the epoch of exclusive machine evolution (prior to biological evolution) is DNA.

Some students, when they begin to study college courses that focus on DNA, know that any DNA molecule is itself not alive:

... DNA is chemical compound ... DNA is non-living, because it is a molecule not an organism ... DNA is not living. It is a chemical - a large fragile molecule ... there is no debate in the biological community about this ...

(Is DNA living or non-living thing?, emphasis added). In other cases, however, students not only harbor the misconception that DNA is alive, they even have to be specially educated to "undo" that misconception:

We are involved in a project to incorporate innovative assessments within a reform-based large-lecture biochemistry course for nonmajors. We not only assessed misconceptions but purposefully

DNA molecule is not alive

changed instruction throughout the semester to confront student ideas. Our research questions targeted student conceptions of deoxyribonucleic acid (DNA) along with understanding in what ways classroom discussions/activities influence student conceptions. Data sources included pre-/post-assessments, semi-structured interviews, and student work on exams/assessments. We found that students held misconceptions about the chemical nature of DNA, with 63 % of students claiming that DNA is alive prior to instruction. The chemical nature of DNA is an important fundamental concept in science fields. We confronted this misconception throughout the semester collecting data from several instructional interventions. Case studies of individual students revealed how various instructional strategies/assessments allowed students to construct and demonstrate the scientifically accepted understanding of the chemical nature of DNA. However, the post-assessment exposed that 40 % of students still held misconceptions about DNA, indicating the persistent nature of this misconception. Implications for teaching and learning are discussed.

(Is DNA Alive?, Research in Science Education, Volume 43, Issue 4, Aug. 2013, pp.1361-1375, emphasis added). As that abstract points out, some students have a difficult time with the concept that a DNA molecule is composed of an arrangement of atoms which are not alive.

That difficulty continues into the concept of molecular machines, that is, it is difficult for us to conceive that atoms and molecules can be configured in such a way that they are actually machines:

The ribosome ... is a large and complex molecular machine, found within all living cells, that serves as the primary site of biological protein synthesis (translation)....

(The Uncertain Gene - 4). That "large and complex molecular machine" is only one among many thousands in cells:

"We took this approach because so many RNAs are rapidly destroyed soon after they are made, and this makes them hard to detect," Pugh said. "So rather than look for the RNA product of transcription we looked for the 'initiation machine' that makes the RNA. This machine assembles RNA polymerase, which goes on to make RNA, which goes on to make a protein." Pugh added that he and Venters were stunned to find 160,000 of these "initiation machines," because humans only have about 30,000 genes. "This finding is even more remarkable, given that fewer than 10,000 of these machines actually were found right at the site of genes. Since most genes are turned off in cells, it is understandable why they are typically devoid of the initiation machinery."

The remaining 150,000 initiation machines -- those Pugh and Venters did not find right at genes -- remained somewhat mysterious.

(The Uncertain Gene - 3). That the complex machinations of DNA and RNA are considered to be of the realm of machines is not new nomenclature.

For example, "machine" or "molecular machine" has been the nomenclature used to describe other non-living entities within cells:

Dr Clarke said: “There are a lot of fundamental questions about the origins of life and many people think they are questions about biology. But for life to have evolved, you have to have a moment when non-living things become living – everything up to that point is chemistry.”
...
“Our cells, and the cells of all organisms, are composed of molecular machines. These machines are built of component parts, each of which contributes a partial function or structural element to the machine. How such sophisticated, multi-component machines could evolve has been somewhat mysterious, and highly controversial.” Professor Lithgow said.
...
Many cellular processes are carried out by molecular ‘machines’ — assemblies of multiple differentiated proteins that physically interact to execute biological functions ... Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.
...
The most complex molecular machines are found within cells.
...
Writing in the journal PLoS Pathogens, the team from Queen Mary's School of Biological and Chemical Sciences show how they studied the molecular machine known as the 'type II bacterial secretion system', which is responsible for delivering potent toxins from bacteria such as enterotoxigenic E. coli and Vibrio cholerae into an infected individual.

Professor Richard Pickersgill, who led the research, said: "Bacterial secretion systems deliver disease causing toxins into host tissue. If we can understand how these machines work, then we can work out how it they might be stopped."

(Do Molecular Machines Deliver Toxins of Power?, emphasis in original). Since RNA and DNA are required for carbon based life forms to exist and to continue to exist, we can argue that DNA is possibly the most evolved entity to have resulted during the epoch of machine evolution.

Before closing today's post, let's consider one of the causal factors leading to the inability of some students to fathom the concept of machine evolution:

Teleology in both science and religion appears in many forms, formats, and verbal expressions during many a dogmatic brainstorm.

Scientists complain that teleological  concepts exist at even the fundamental levels of our modern science (compare If Cosmology Is "Off," How Can Biology Be "On?" with The Uncertain Gene - 2).

In the series The Uncertain Gene, Dredd Blog posts attempt to discuss a pure, i.e. teleology free, account concerning issues about how abiotic machine-evolution intersects with biotic carbon-based-life-form evolution through the advent of the quantum tunneling dynamics of protons.

Specifically, I am referring to proton tunneling at the location of certain hydrogen bonds in gene related molecules (The Uncertain Gene).

(Weekend Rebel Science Excursion - 24). Teleological language is a problem because its users subconsciously or consciously use verbiage that connotes essences to machines or organisms which those machines or organisms do not have:

Since at least the 17th century (and mostly because of Newton), natural scientists have stopped using formal or final causes to explain natural phenomena ... except in biology. This was first pointed out by Colin Pittendrigh (Pittendrigh, C. S. Behavior and Evolution) (ed. by A. Rose and G. G. Simpson), Yale University Press, 1958), who coined the term "teleonomy" to refer to the kind of teleological phenomena observed in biological processes.
...
So, let's get back to the book (Quantum Aspects of Life) to further emphasize that physicists also can get loose with their discipline, i.e. can get off into the weeds of teleology, unless they are careful:

Expressed differently, how does a quantum superposition recognize that it has “discovered” life and initiate the said collapse? There seems to be an unavoidable teleological component involved: the system somehow “selects” life from the vastly greater number of states that are nonliving ... But this implies the environment somehow favours life—that life is “built into” nature in a preordained manner. So an element of teleology remains. (p. 11) ... an element of teleology is required; namely that the molecule must somehow know before hand what it is aiming for. (p. 42) There is no teleology needed here since we describe the measurement as a two-step process ... (p. 45) ... there’s the teleological point that, hey, we search for something ... (p. 357) ... As far as the teleological aspects are concerned (p. 360) ... Teleological aspects and the fast-track to life ... there is a teleological issue here ... (p. 392)

(ibid, Quantum Aspects of Life, emphasis added). The point being made is that "natural selection" discussions by either evolutionary biologists or physicists can become fundamentally teleological unless great care and focused technical language skills are employed ...

(The Uncertain Gene - 2). For those who want to go through that experiment, describe the machine epoch, beginning at the Big Bang then progressing through some ~10.21 billion years of machine evolution until finally molecules of DNA became part of the universe of machines, all of which transpired prior to the advent of any carbon based life forms.

Don't leave out some of E.O. Wilson's pleas for discourse and nomenclature on the evolution of morality, altruism, and ethics, especially as it has been considered on Ecocosmology Blog in the same vein that abiotic intelligence has been considered:

The stars like our Sun, at the center of all solar systems, will support life forms for an amount of time, but will then destroy life on the planets near them at an unknown time during each solar system's developmental life cycle.
...
This could be read to imply that abiotic evolution includes a process whereby undesirable carbon based biotic life forms that might later evolve will eventually be extinguished, will "automatically" become extinct, should they evolve/develop primarily "maladjusted behaviors."
...
It would seem to imply, then, the existence of some form of abiotic intelligence intent on preventing future undesirable biotic evolution from getting out of hand and populating the cosmos with undesirables

(Did Abiotic Intelligence Precede Biotic Intelligence?). How could any one describe "what is up with that", in terms of morality, ethics, and/or altruism, by using the nomenclature and theory of a "natural selection" apparatus which results in the mass murder extinction (Tenet One Basics) of innocent and/or helpless species?

Nevertheless, be sure to use the nomenclature of natural selection as your linguistic word source to describe machine evolution: beginning at energy evolving into subatomic particles like protons, then those subatomic particles evolving into atoms, the atoms into molecules, then molecules into compounds, then compounds into dust clouds which condense into planetoids, which eventually evolve into stars that create carbon within themselves, then release that carbon when those stars "go nova" or "go supernova."

You will find that you will encounter some teleological problems, just like the physicists in the book Quantum Aspects of Life who tried a similar teleological-language-free task (ibid).

For example consider the use of the word "behavior":

be·hav·ior

1. manner of behaving or acting.
2. Psychology, Animal Behavior.

a. observable activity in a human or animal.
b. the aggregate of responses to internal and external stimuli.
c. a stereotyped, species-specific activity, as a courtship dance or startle reflex.

3. Often, behaviors. a behavior pattern.
4. the action or reaction of any material under given circumstances: the behavior of tin under heat.

(Dictionary). The quanta (e.g. electrons, photons, protons, neutrons) will have "behavior" ... which carbon based life forms will also have ... so be careful that teleological language does not subvert your nomenclature:

On one planet — a most ordinary planet, orbiting a mediocre star, one speck on the spiral arm of a standard galaxy — surging continents and roiling oceans organized themselves, and out of the oceans an ooze of organic molecules reacted and built proteins, and life began.

(The God Particle, Lederman, p. 1, bold added). The assertions "organized themselves" and "reacted and built" are teleological slips (or are they inferences that abiotic intelligence existed?) that reflect a need for better nomenclature.

For another example, if you think "genes are selfish" you may tend to explain machine evolution in terms like "machines are selfish" (because genes are simply molecular machine entities which are not alive).

The language of that thought experiment could be extrapolated, if you are not careful, to a notion of "protons that became selfish" ... so those selfish genes protons gathered an electron to themselves to form a hydrogen atom.

Then later they became more selfish and therefore gathered a neutron to themselves too, so as to form other atoms.

Then atoms became selfish and gathered other atoms to themselves to form molecules, etc. etc.

With such contemplation you may expose more flaws in such teleological practices, which exposure may lead to some form of improvement over flawed historical teleological communications and misunderstandings (looking on the bright side that could lead to some remedy in the form of scientifically sound and improved nomenclature).

The next post in this series is here, the previous post in this series is here.

What Kind of Intelligence Is A Lethal Mutation?

Lethal Mutation?

Regular readers know that several recent series on Ecocosmology Blog have dealt with various concepts of intelligence as well as variations within several "types of intelligence."

For example, in What Kind of Intelligence Is Prescience? and What Kind of Intelligence Is Prescience? - 2 we looked at ancient writings of two well known religions to contemplate intelligent ancient views of environmentalism which seem to be prescient.

In Did Abiotic Intelligence Precede Biotic Intelligence? we contemplated whether or not there are two types of intelligence as well as which type came first.

In the series Putting A Face On Machine Mutation we lament the dearth of peer reviewed papers (compared with those on biological evolution) concerning molecular-machine evolution in the context of the evolution of intelligence.

Today, we are going to indulge the notion of noted American biologist Ernst Mayr, who unabashedly hypothesized that human intelligence is a lethal mutation which is likely to lead to the extinction of the human species, as well as most other species on the planet Earth.

Let's begin with a debate between astrophysicist Carl Sagan and the American biologist Ernst Mayr; two scientists who saw human intelligence in a different light:

I'LL BEGIN with an interesting debate that took place some years ago between Carl Sagan, the well-known astrophysicist, and Ernst Mayr, the grand old man of American biology. They were debating the possibility of finding intelligent life elsewhere in the universe. And Sagan, speaking from the point of view of an astrophysicist, pointed out that there are innumerable planets just like ours. There is no reason they shouldn't have developed intelligent life. Mayr, from the point of view of a biologist, argued that it's very unlikely that we'll find any. And his reason was, he said, we have exactly one example: Earth. So let's take a look at Earth. And what he basically argued is that intelligence is a kind of lethal mutation ... you're just not going to find intelligent life elsewhere, and you probably won't find it here for very long either because it's just a lethal mutation ... With the environmental crisis, we're now in a situation where we can decide whether Mayr was right or not. If nothing significant is done about it, and pretty quickly, then he will have been correct: human intelligence is indeed a lethal mutation. Maybe some humans will survive, but it will be scattered and nothing like a decent existence, and we'll take a lot of the rest of the living world along with us.

(Human Intelligence and The Environment, Dr. Noam Chomsky, 9/30/10). Dr. Chomsky argues that Dr. Mayr had a good point if we take into consideration our "intelligent" use of the Earth's resources, including producing weapons of mass destruction, like hydrogen bombs and other nuclear weapons that threaten the existence of life on Earth.

Which brings to mind the photo of Dr. Einstein at the top of the post, in as much as it was his intelligence in large part that made weapons of mass destruction and human extinction possible.

The Tenets of Ecocosmology counsel against the improper use of the Earth's environment in any way, urging instead that all species contain some germane bit of information which humanity is likely to need in order to continue to exist.

The Toxins of Power Blog cautions that the source of toxins that do damage to intelligence so as to render it lethal, arise only in the presence of a certain type of power.

---

---

Did Abiotic Intelligence Precede Biotic Intelligence?

Bright Things

I suppose we should also ask ourselves whether or not abiotic intelligence even exists.

If it does, since abiotic evolution preceded biotic evolution in our theoretical models, then that factor answers our question.

Nevertheless, either way it seems to require another discussion about what intelligence in general actually is, and whether it is the same in the abiotic realm as it is in the biotic realm.

It is a subject that is coming up a bit more regularly of late than it used to, when the notion of "intelligence" was limited exclusively to the small realm of human consciousness (see e.g. On The Peak of Intelligence - 2).

One can expect arguments both for and against abiotic intelligence, if we consider and extrapolate on Tenet One, which is:

The stars like our Sun, at the center of all solar systems, will support life forms for an amount of time, but will then destroy life on the planets near them at an unknown time during each solar system's developmental life cycle.

(The Tenets of Ecocosmology, Tenet One). According to our current cosmological evolutionary models, stars evolved during the long abiotic evolutionary phase that preceded the much shorter biotic evolutionary phase (see e.g. Putting A Face On Machine Mutation - 3).

In those models "stars" evolved (On the Origin of the Genes of Viruses - 6) then produced carbon within them, which is the basis of biotic life and therefore biotic evolution (e.g. Logic of Metabolism).

Stars evolved such that they made carbon based life possible, yet they will eventually destroy all the life in the habitable zone of planets near them; life which they originally made possible:

Earth's fate is precarious. As a red giant, the Sun will have a maximum radius beyond the Earth's current orbit, 1 AU (1.5×10¹¹ m), 250 times the present radius of the Sun. However, by the time it is an asymptotic giant branch star, the Sun will have lost roughly 30% of its present mass due to a stellar wind, so the orbits of the planets will move outward. If it were only for this, Earth would probably be spared, but new research suggests that Earth will be swallowed by the Sun owing to tidal interactions. Even if Earth would escape incineration in the Sun, still all its water will be boiled away and most of its atmosphere would escape into space.

(Life According To Science). Before this "catastrophe" happens there is sufficient time for life forms to learn space travel and find a new home world, if:

That final catastrophic event (destruction of life on inner planets), and all events leading up to it, comprise "The Test" (This test is composed of all the preliminary and final evolutionary requirements for the life forms on all planets near central stars. The Test works as a wall, moat, or barrier, to divide those species who may continue to live in the physical universe from those who may not).

(The Tenets of Ecocosmology, Tenet Two). This could be read to imply that abiotic evolution includes a process whereby undesirable carbon based biotic life forms that might later evolve will eventually be extinguished:

"The more I examine the universe and study the details of its architecture, the more evidence I find that the universe must have known that we were coming."

(Disturbing the Universe,  by Freeman Dyson, 1979). That is, will biotic forms that evolve "automatically" become extinct in the event that they evolve/develop primarily "maladjusted behaviors?"

The notion would would seem to imply, then, the existence of some form of abiotic intelligence intent on preventing future undesirable biotic evolution from getting out of hand and populating the cosmos with undesirables:

To pass The Test, intelligent life forms inhabiting any planet will be required to:

a) first learn to live and work together within, and in accord with, their planet's ecosystem, and to substantially coexist with all the other species on that planet, while overcoming any toxins of power that are contrary to social harmony;

b) develop technology that produces space vehicles able to substantially meet or exceed the speed of light;

c) find another solar system with a habitable planet which contains a central star still having enough time left in its stellar life cycle for them to colonize a habitable planet in that solar system (since it is unknown whether the toxins of power are to be found on all planets, as they are found on Earth, that possibility should be taken into consideration when selecting any new planet or moon as a home world); Note: since red dwarfs are the most stable and most abundant stars, they should be favored over Sun-like stars;

d) colonize that habitable planet, and then improve ecocosmological skills as needed;

e) then repeat the entire process ad infinitum;

f) or, experience a morph into another "species" free from that type of solar/planetary cosmic dependence.

(The Tenets of Ecocosmology, Tenet Three). We reviewed the cosmological evolutionary model of The Big Bang Theory recently, which notably indicates that abiotic evolution is a much older evolutionary process than biotic evolution is.

Abiotic evolution takes up by far the greatest portion of time involved when considering the span of time involved for all of evolution (Putting A Face On Machine Mutation - 3).

The fundamental essence which The Tenets of Ecocosmology indicate as being built into this abiotic and biotic evolutionary dynamic is a command of due respect for all life forms:

The seeds of intelligence (genetic and memetic clues) required to successfully perform The Test are distributed into all species, races, religions, sciences, creeds, and genders. Thus, all individuals should be respected as carriers of some quanta of the seed of intelligence required to pass The Test, lest a fundamental quantum of necessary intelligence be lost.

(The Tenets of Ecocosmology, Tenet Four). Thus, the evolutionary path seems to begin with abiotic evolution of a non-living system that can provide the necessary ingredients of later biotic life.

But more than that, it also contains fundamental processes and/or mechanisms for judging some fundamental aspects of the competence of that later-to-begin biotic evolution.

That would seem to be a form of intelligent "non-life," but let's keep our notion subject to the difficulty of defining "life" and "machine":

The definition of life is as enormous a problem as the phenomenon of life itself. One could easily collect from the literature more than 100 different definitions, none satisfactory enough to be broadly accepted. What should the definition contain, to be suitable for all varieties of observable life? Humans, animals, plants, microorganisms. Do viruses also belong to life?

...

“Our cells, and the cells of all organisms, are composed of molecular machines. These machines are built of component parts, each of which contributes a partial function or structural element to the machine. How such sophisticated, multi-component machines could evolve has been somewhat mysterious, and highly controversial.” Professor Lithgow said.

(Putting A Face On Machine Mutation - 3). The machines that preceded life, and of which life is based, could be said to have evolved in an abiotic process that has some of the hallmarks of "some type of intelligence."

Especially when we are not reluctant to use the term "machine intelligence" to describe the software that comprises the "brains" of computers.

Not a very easy subject to derive only one clear dialogue is it?

Let's really muddy the waters, then, by pointing out that some religions are antithetical to this structure which The Tenets of Ecocosmology set forth above, a structure which favors appreciation of Nature.

This favoring of Nature is not the way of everyone's science or religion:

"Now I notice a very odd point. All other religions in the world, as far as I know them, are either nature religions, or anti-nature religions ... But here is something quite different. Here is something telling me - well, what? Telling me that I must never ... say that death does not matter." - C.S. Lewis

(God in the Dock: Essays on Theology and Ethics, page 86). Now that you have been given some food for thought, have fun with it!

Putting A Face On Machine Mutation - 3

The machine age came first

The oft asked question: "Which came first, the chicken or the egg?" is actually a common mistake that both scientists and laypersons alike can make.

A more relevant question: "Which came first machines or biological organisms?" is less often contemplated, so, in this series we have been exploring the realm of time prior to "life", a time before a border line existed between machine and organism.

That is, before the border line between abiotic and biotic, which are defined as:

abiotic: a·bi·ot·ic [ey-bahy-ot-ik, ab-ee-] adjective-
of or characterized by the absence of life or living organisms. (Dictionary).

biotic: bi·ot·ic [bahy-ot-ik] adjective-
pertaining to life. (Dictionary).

As it turns out the "border line" between the two is actually a great chasm of not only space, but of time as well.

This is quite important because the biotic realm is carbon based, and therefore could not, according to cosmological evolution, come into existence prior to carbon having been formed in stars.

Carbon was formed in stars late in the abiotic epoch, via the Triple-alpha process.

The lighter elements had to first evolve from primitive energy, which cooled soon afterwards to a temperature too cool for carbon to form.

That whole early era of evolution is described and detailed by evolutionary cosmology, not biological evolution (On the Origin of the Genes of Viruses - 6).

It covers a vast amount of time compared to biological evolution, which only covers a fraction of the span of time that abiotic evolution covers.

To illustrate, let's review some of that theory from zero to the advent of carbon in stars:

The Big Bang theory is the prevailing cosmological model that describes the early development of the Universe. According to the Big Bang theory, the Universe was once in an extremely hot and dense state which expanded rapidly. This rapid expansion caused the Universe to cool and resulted in its present continuously expanding state. According to the most recent measurements and observations, the Big Bang occurred approximately 13.75 billion years ago, which is thus considered the age of the Universe. After its initial expansion from a singularity, the Universe cooled sufficiently to allow energy to be converted into various subatomic particles, including protons, neutrons, and electrons. While protons and neutrons combined to form the first atomic nuclei only a few minutes after the Big Bang, it would take thousands of years for electrons to combine with them and create electrically neutral atoms. The first element produced was hydrogen, along with traces of helium and lithium. Giant clouds of these primordial elements would coalesce through gravity to form stars and galaxies, and the heavier elements would be synthesized either within stars or during supernovae.

(The Big Bang Theory, emphasis added). The Earth is said to have formed  "around 4.54 billion ... years ago" (History of Earth).

Therefore The Big Bang happened about 9.21 billion years before the Earth formed (13.75 - 4.54 = 9.21).

Biological organisms formed on the Earth about a billion years later, which would be ~10.21 billion years after The Big Bang.

Humans, homo sapiens,  are said to have evolved about 200,000 years ago, which would be ~13.7498 billion years after The Big Bang (13.7498 + 00.0002 = 13.75 billion years). Homo sapien evolution is a very tiny 0.0002 billion years of the 13.75 billion year story.

The abiotic epoch which preceded the biotic epoch involved a vast amount of "time" as we know it, populating vast areas of space with the atoms that make up chemicals, the subject of the scientific discipline Chemistry:

Dr Clarke said: “There are a lot of fundamental questions about the origins of life and many people think they are questions about biology. But for life to have evolved, you have to have a moment when non-living things become living – everything up to that point is chemistry.”
...
“Our cells, and the cells of all organisms, are composed of molecular machines. These machines are built of component parts, each of which contributes a partial function or structural element to the machine. How such sophisticated, multi-component machines could evolve has been somewhat mysterious, and highly controversial.” Professor Lithgow said.
...
Many cellular processes are carried out by molecular ‘machines’ — assemblies of multiple differentiated proteins that physically interact to execute biological functions ... Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.
...
The most complex molecular machines are found within cells.
...
Writing in the journal PLoS Pathogens, the team from Queen Mary's School of Biological and Chemical Sciences show how they studied the molecular machine known as the 'type II bacterial secretion system', which is responsible for delivering potent toxins from bacteria such as enterotoxigenic E. coli and Vibrio cholerae into an infected individual.

Professor Richard Pickersgill, who led the research, said: "Bacterial secretion systems deliver disease causing toxins into host tissue. If we can understand how these machines work, then we can work out how it they might be stopped."

(Do Molecular Machines Deliver Toxins of Power?). The gist of this is that the era of the evolution of machines is just another way of saying the epoch of abiotic evolution.

Let's look at the sequence again:

1) universe exists as singularity like a hot plasma;

2) a big bang or explosion takes place;

3) parts of 'primitive machines' evolve (electrons, protons, and neutrons);

4) machines (atoms of "the elements") evolve from primitive parts;

5) elements/machines evolve into star machines (Suns);

6) star machines produce carbon, the basis of biotic forms;

7) finally, machines evolve into carbon based organisms (the biotic epoch begins).

This sequence may appear simple at first blush, but is not as simple as it first appears to be, because it contemplates an exploration of the border line between life and non-life:

The definition of life is as enormous a problem as the phenomenon of life itself. One could easily collect from the literature more than 100 different definitions, none satisfactory enough to be broadly accepted. What should the definition contain, to be suitable for all varieties of observable life? Humans, animals, plants, microorganisms. Do viruses also belong to life?

(What Is Life, The Scientist). Once we reach the cellular level, microbes, the jump to multicellular is easier to follow, in most cases, than the jump from abiotic to biotic (see Evolving Multicellularity).

Most scenarios one reads concerning evolution begin with biotic life already existing, then proceed from there.

Thus, the big picture of ~10.21 billion years of abiotic evolution which preceded that much smaller ~3.54 billion years of biotic evolution is often ignored or given short shrift.

---

Richard Dawkins interviews Steven Rose (minutes:seconds):

00:35 natural selection is only one process or part of evolution, not the exclusive process or part ...

01:20 organisms take part in the selection of their environment ...

03:30 Rose takes issue with the overuse of the gene as the most important element in evolution ...

04:10 entire organisms must change, not simply individual genetic parts of it ...

05:20 Rose does not think that genes pass themselves from one generation of a species to the next; rather he thinks the information is passed, but that the organism then produces genetic material from that information ...

05:25 Rose says the idea than genes replicate themselves is not true; the orchestra of the entire cell is what replicates the genes, the DNA ...

08:20 the cell decides which parts of the DNA, the genes, to turn on and off ...

10:30 Rose indicates that focus one only one molecule, the DNA molecule, the gene, leads down inaccurate pathways; the solution is to see the organism as an entire functioning entity with equal emphasis on the parts, not unequal emphasis on the genetics alone ...

---

---

The next post in this series is here, the previous post in this series is here.

Putting A Face On Machine Mutation - 2

When we speak of "life" or "the cosmos", starting our discussion at "the beginning" is difficult.

Especially when, in some ways, "the beginning" is as illusive to us as defining or grasping the meaning of "a line."

Wikipedia tells us that "a line" can extend to infinity, in either direction, having no beginning, and no end.

Or "a line" can be finite in both directions, having one point described as the "beginning point", with another point being described as the "end point".

Still, those two points exist on that other "line" which, as I said, has no beginning point and no end point.

Interestingly, "a line segment" has the same property as one type of line, that is, it has both a beginning point and an end point.

When a beginning point exists, but no end point exists, then the entity is not called "a line segment" or "a line", instead it is called "a ray."

In the first post of this series we dealt with "the beginning", in the sense that plane geometry deals with it, i.e., somewhat like the discussion of "a line."

We looked at where life begins, not in the sense of time, not in the sense of the past or future, but in the sense of locus, that is, where in terms of location, does the "machine" world end, and the world of "life" begin?

To be sure, in this series we have set forth a valid reason to equate "machine" with "inorganic", likewise to equate "life" with "organic":

"Our cells, and the cells of all organisms, are composed of molecular machines. These machines are built of component parts, each of which contributes a partial function or structural element to the machine. How such sophisticated, multi-component machines could evolve has been somewhat mysterious, and highly controversial." Professor Lithgow said.
...
"François Jacob described evolution as a tinkerer, cobbling together proteins of one function to yield more complex machines capable of new functions." Professor Lithgow said.

"Our work describes a perfect example of Jacob's proposition, and shows that Darwin's theory of evolution beautifully explains how molecular machines came to be."

(ibid, quoting Science Daily and Monash Univ.). Our science describes those "component parts" of molecules with the word "atoms", which are said to be the smallest unique identifier of  what our science calls "the elements."

What we call "simple cells" are said to be complex molecular machines (inorganic) with something more, hence, more complex organization (organic).

Thus, in this context when we ask about "the beginning", we are simply asking "when we use super microscopes and/or other tools for looking deep into the micro world which our eyes alone cannot detect, where does the 'machine' essence end, and where does the 'organic' essence begin?"

In some cases the answer to that question will depend on definition, on nomenclature.

It probably behooves us to substitute "boundary" in place of "beginning", when we discuss "machine" or "life", at least in the context of locus.

So, concerning inorganic machine entities compared with organic life, our nomenclature should change as scientific discoveries improve to bring us results that boil down to a better scientific understanding.

Einstein once said: "Make everything as simple as possible, but not simpler" (paraphrased "don't oversimplify").

Based upon the statements of Professor Lithgow, above, we can define two categories of entities, machine (inorganic) and life (inorganic bound with organic).

In that sense, all plants, animals, and elements are either "machine" or "life", it is just that "life" in this nomenclature is "machines bound to additional organic essence", and "machine" in this nomenclature is "atoms and/or molecules without organic essence", or as a recent comment by a scientists indicates:

Dr Clarke said: “There are a lot of fundamental questions about the origins of life and many people think they are questions about biology. But for life to have evolved, you have to have a moment when non-living things become living – everything up to that point is chemistry."

(Univ. of York, cf Organic & Biomolecular Chemistry). So, for purposes of this discussion, looking into our super microscope at the lowest level of the machine world, we will see atoms, then moving up a level we will see atoms organized into molecules, then moving up another level we will see very complex molecules, then at the level where we approach the boundary between machines and where life begins, we will see a very complex molecular machine with something more, something that transforms it into life, a super complex machine with super organization, something we call organic, then eventually we reach the level of "a cell" (cf. Are Toxins of Power Machines Or Organisms?).

Leaving the concept of boundaries, now turning to concepts of "the beginning" in terms of time, The Big Bang Theory (conceived of by a Belgian Priest) deals with "the beginning" in that context.

There is a specific term used to define "the beginning" of elements in the sense of time, thus the beginning of machines in the sense of time, which is called Big Bang Nucleosynthesis.

Following nucleosynthesis, in time sequence, more complex machines developed, which we call stars.

Going on in time sequence in Big Bang cosmology, once those stars formed they then produced even more elements, i.e., more machines.

Clearly then, cosmological evolution advocates and hypothesizes that machines replicated, and/or formed other machines, in the earliest evolutionary processes of The Big Bang.

This is a good place, then, to characterize machines as being able to replicate other machines, but to characterize organics as being able to reproduce their own kind, but change through morphing.

Machines replicate not only their own kind, but other kinds of machines, but observation gives us evidence that life, in its organic reproductive process, reproduces only its own kind but experiences morph from time to time.

This is also a good place to mention that the combination of machine and organic is really what science fiction likes to call "a cyborg", a combination of inorganic machine with non-machine organics.

But, we can also see that organics cannot exist without the underlying machine foundation which organics extend upon.

We can also note that death, then, is the removal of the organic essences, so that the entity can revert back to the purely inorganic (machine) components underneath the organic level.

The next post in this series is here, the previous post in this series is here.

Will Humans Evolve "Further"?

Evolutionary studies and papers over the past few months and years, as well as the Tenets of Ecocosmology, would give new meaning to the word "further" contained in the question presented in the title of this post.

One article asks "Are Humans Still Evolving?", another answers "Humans Will Not Evolve Further", one asks "Natural Selection Not The Only Process That Drives Evolution?", while yet another exclaims "Natural Selection May Not Produce The Best Organisms", and finally as one says "Darwin Had It Right".

Notice some of the obviously conflicting statements in these articles:

"Survival of the fittest" is the catch phrase of evolution by natural selection. While natural selection favors the most fit organisms around, evolutionary biologists have long wondered whether this leads to the best possible organisms in the long run. [article 1]

...

As part of a working group sponsored by the National Evolutionary Synthesis Center in Durham, NC, the team of researchers decided to find out if natural selection — a major driving force of evolution — is still at work in humans today. The result? Human evolution hasn't ground to a halt. [article 2]

...

The results lead to the provocative hypothesis that, rather than being the result of Darwinian selection for new adaptations, many of the genetic changes leading to human-specific characters may be the result of the fixation of harmful mutations. This contrasts the traditional Darwinistic view that they are the result of natural selection in favour of adaptive mutations. [article 3]

(ibid). Debate is even developing around the issues resolved or not resolved by Darwinius and Afradapis, two finds this summer. It seems clear to me, then, that the teaching criteria for determining what is "the better" is what is drifting, evolving, or at least changing.

You may want to read some other concepts of other top scientists about where human evolution is heading; will we evolve into robots or into super human beings?

There is no set formula to determine, to use Darwin's approved language, "the fittest", if these fundamental questions are still perplexing to scientists.

One thing is sure, the criteria are biological considerations based upon this planet alone. The criteria, therefore, tend to be geocentric like they were when the earth was thought to be the center of the universe.

There are greater determinants, which seal the fate of species on planets orbiting central stars, than the singular and quite limited notion of biological evolution.

According to the Tenets of Ecocosmology, biological evolution on habitable planets is by no means the greatest factor in passing "The Test".

That test must be passed via memetic evolution in order for sentient species to avoid extinction in this cosmos, even after having avoided extinction on a habitable planet.

Will Humans Evolve Into Machines?

Tenet 3(f) of Ecocosmology recognizes that if the human species morphs or evolves into a species that does not depend on central stars with habitable planets orbiting them, the need for infinite nomadic travel from solar system to solar system can be avoided.

This blog also questioned the issue of machines in the scheme of evolution in a post Putting a Face on Machine Mutation a while back.

The notion of evolution into machines seems like science fiction, however, some serious and viable scientists think human evolution into machines is the only viable reality for survival of the human species:

In a futuristic mode similar to Hawking, both Steven Dick, chief NASA historian and Carnegie-Mellon robotics pundit, Hans Moravec, believe that human biological evolution is but a passing phase: the future of mankind will be as vastly evolved sentient machines capable of self-replicating and exploring the farthest reaches of the Universe programmed with instructions on how to recreate earth life and humans to target stars.

Dick believes that if there is a flaw in the logic of the Fermi Paradox, and extraterrestrials are a natural outcome of cosmic evolution, then cultural evolution may have resulted in a post-biological universe in which machines are the predominant intelligence.

(Space Colonization). In the post Putting a Face on Machine Mutation linked to above, there is a discussion about machines evolving into biotic organisms many millions of years ago:

"Our cells, and the cells of all organisms, are composed of molecular machines. These machines are built of component parts, each of which contributes a partial function or structural element to the machine. How such sophisticated, multi-component machines could evolve has been somewhat mysterious, and highly controversial." Professor Lithgow said.

...

"François Jacob described evolution as a tinkerer, cobbling together proteins of one function to yield more complex machines capable of new functions." Professor Lithgow said.

"Our work describes a perfect example of Jacob's proposition, and shows that Darwin's theory of evolution beautifully explains how molecular machines came to be."

(Science Daily, emphasis added; cf Putting A Face On Machine Mutation - 4). But wouldn't reverse evolution from biological human back into machines violate Dollo's law? Isn't reverse evolution illegal? Note:

The Belgian biologist Louis Dollo was the first scientist to ponder reverse evolution. “An organism never returns to its former state,” he declared in 1905, a statement later dubbed Dollo’s law.

(NY Times). Well, that throws a monkey wrench into the equation doesn't it?

Wouldn't you know that some futurists are claiming that only the rich will evolve into machines as a separate species?

Can The First Bank of Reincarnation be far behind?

Putting A Face on Machine Mutation

Dredd Blog has a post, which focuses on the issue of the evolution of machines.

Surprisingly, there is more to the question this issue deals with than what at first appears.

It is a post which asks the question: "which came first organic species or machine species?":

Looking at it that way, the machines are at the foundation of biological organisms aren't they? We are in a sense cyborg, then, because we are both machine and organic.

We are composed of atoms and elements which are organized in such a way that they morph into organisms. Organization.

So goes the cosmological theory of machines mutating into "higher forms". Atomic quanta which are composed of non-organic mass and non-organic energy, and therefore are machines, morph or evolve into other machines we call atoms and elements. Then those elements morph into molecules which morph or evolve into organic, biological life forms.

What is puzzling in many ways is that this is called both science fiction and evolutionary science. What makes it fiction on the one hand, but science on the other hand, on the same set of facts? By facts I mean machines morphing or evolving into biological organisms.

(Putting A Face on Machine Mutation, emphasis added). New research tends to agree with the position that the machines came first:

"Our cells, and the cells of all organisms, are composed of molecular machines. These machines are built of component parts, each of which contributes a partial function or structural element to the machine. How such sophisticated, multi-component machines could evolve has been somewhat mysterious, and highly controversial." Professor Lithgow said.

...

"François Jacob described evolution as a tinkerer, cobbling together proteins of one function to yield more complex machines capable of new functions." Professor Lithgow said.

"Our work describes a perfect example of Jacob's proposition, and shows that Darwin's theory of evolution beautifully explains how molecular machines came to be."

(Science Daily, emphasis added; cf. Monash Univ.). When you look at your wrist watch or your cell phone you may have more resistance to the notion that a machine evolves, yet the fly you just swatted away (which is far more complex) does not make you so skeptical.

That is one reason we bring these issues up, so that we do not fall asleep at the wheel and believe anything that comes our way.

With that in mind, notice how they came up with this new notion that machines do evolve:

"Our cells literally are chimeras of a "host" cell and these intracellular bacteria. Yet bacteria don't have TIM complexes – to understand where the TIM complex came from we simply applied scientific reasoning and looked at a modern-day bacterium akin to the organism that gave rise to mitochondria." Professor Lithgow said.

(ibid, Science Daily, emphasis added). Uh oh, the "scientific reasoning" statement, which we found in another post, can be translated "have faith" at times.

Even scientists balk at the faith of their peers at times, which this blog pointed out, and why not, since that is called "peer review".

We will keep watching and reporting these issues for your perusal, and your decision as to which came first, the machine or the organism.

The next post in this series is here.