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Author Topic:   An ID hypothesis: Front-loaded Evolution
Genomicus
Member (Idle past 1261 days)
Posts: 852
Joined: 02-15-2012


Message 16 of 216 (653249)
02-19-2012 2:35 PM
Reply to: Message 14 by Theodoric
02-19-2012 2:27 PM


quote:
Oh a quick search shoes "word salad" is the accepted spelling. You have a source that shows otherwise?

I stand corrected.


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Jon
Inactive Member


Message 17 of 216 (653250)
02-19-2012 2:36 PM
Reply to: Message 7 by Genomicus
02-19-2012 12:56 PM


Re: An ID hypothesis: Front-loaded Evolution
The difference here, of course, is that one evolutionary trajectory is planned, while the other is simply the result of contingency.

Not true at all. Random mutations are anything but random. The mutations possible are constrained by the nature of the DNA molecules and their chemical and structural relationships to one another. Expectant mothers everywhere can rest assured that whatever horrible afflictions might plague their newborn, the child's carbon atoms being replaced by hydrogen atoms—a truly random event—will not be one of them.

The physical, biological, and chemical 'laws' of the Universe are pretty much the only predetermined biases in play. And they seem quite capable of keeping things in order on their own.

Note, however, that any supposed poor design must be thoroughly analyzed before concluding that no rational designer would have done it that way.

Of course not. There's no need to look for a designer under every rock. That'd be a foolish waste of time.

Precisely because a phylogenetic tree consisting of sub-optimal codes in basal lineages is not what we would expect under front-loading; we would expect a universal optimal genetic code (or several optimal genetic codes), not a phylogenetic tree of genetic codes like I describe above. I guess it's not quite accurate to say "that it does not exist is evidence in favor of the front-loading hypothesis." Better would be: that there is a universal optimal genetic code, instead of a phylogenetic tree of genetic codes (as I describe above), is evidence in favor of the front-loading hypothesis? Why? Because it is expected under the FLE model. We'd predict that the first designed genomes were highly optimized such that when complex life forms do appear on the scene, they don't have to cope with a sub-optimal code, which could even lead to their extinction.

What can be inferred about the nature of the supposed designer(s) based on this, and what can that add to our understanding of genesis?

Jon


Love your enemies!

This message is a reply to:
 Message 7 by Genomicus, posted 02-19-2012 12:56 PM Genomicus has replied

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Genomicus
Member (Idle past 1261 days)
Posts: 852
Joined: 02-15-2012


Message 18 of 216 (653252)
02-19-2012 2:39 PM
Reply to: Message 15 by jar
02-19-2012 2:31 PM


Re: more just plain incorrect assertions.
quote:
There is no such thing as "a universal optimal code", that is simply another example of your making stuff up.

I cited Freeland et al., 2000, to support the assertion that the canonical, universal genetic code is highly optimized. I am not making that up, at all.

quote:
There is no FLE hypothesis yet other than the unsupported assertion that YOU think there is some planner or plan.

The assertion is backed up by clues like the universal optimal genetic code.

quote:
And as I said in the very beginning of this thread, you offered no predictions or any possible tests that would not be satisfied by pointing how well the puddle fits the water.

Let's start with one of the FLE predictions. The FLE hypothesis predicts that genes important for the development and function of multicellular organisms will share deep homology with prokaryotic genes. How is this an example of "pointing how well the puddle fits the water"?


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 Message 15 by jar, posted 02-19-2012 2:31 PM jar has replied

Replies to this message:
 Message 20 by jar, posted 02-19-2012 2:59 PM Genomicus has replied

  
Genomicus
Member (Idle past 1261 days)
Posts: 852
Joined: 02-15-2012


Message 19 of 216 (653255)
02-19-2012 2:45 PM
Reply to: Message 17 by Jon
02-19-2012 2:36 PM


Re: An ID hypothesis: Front-loaded Evolution
quote:
Not true at all. Random mutations are anything but random. The mutations possible are constrained by the nature of the DNA molecules and their chemical and structural relationships to one another. Expectant mothers everywhere can rest assured that whatever horrible afflictions might plague their newborn, the child's carbon atoms being replaced by hydrogen atoms—a truly random event—will not be one of them.

Are you suggesting that if FLE has not occurred, then the evolutionary trajectories were still planned? That really does not make sense. The difference between FLE trajectories and non-teleological trajectories is that the former is planned, while the latter is not. Of course, in both instances, natural laws constrain the course of evolution - but the latter is not planned.

quote:
That'd be a foolish waste of time.

That's more a subjective opinion, is it not?

quote:
What can be inferred about the nature of the supposed designer(s) based on this...

Based on this, it can be inferred that the designers are rational agents - advanced nanotechnologists who have the capability to design the genetic code such that it is optimal.

quote:
...and what can that add to our understanding of genesis?

Why should it add something to our understanding of Genesis? Why did an ancient text suddenly get involved in our discussion?


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jar
Member
Posts: 33957
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.0


(2)
Message 20 of 216 (653257)
02-19-2012 2:59 PM
Reply to: Message 18 by Genomicus
02-19-2012 2:39 PM


Re: more just plain incorrect assertions.
That is simply not a prediction, just word salad. It is no different than saying the puddle was shaped to hold the water. It is just a nonsense assertion.

If you actually had read Stephen Freeland's work you would know that he has said 'that despite the continuing and widespread use of the phrase "universal genetic code", no such thing exists.'

Not only is there no such thing as a universal genetic code, there is no indication that any genetic code is 'optimal' other then within the confines of that particular incident, just as the puddle is perfectly shaped to hold the water and the water fits optimally within the bounds of the puddle. In addition it is optimally placed to reflect the trees.


Anyone so limited that they can only spell a word one way is severely handicapped!

This message is a reply to:
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Replies to this message:
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Granny Magda
Member (Idle past 154 days)
Posts: 2384
From: UK
Joined: 11-12-2007


Message 21 of 216 (653258)
02-19-2012 3:02 PM
Reply to: Message 1 by Genomicus
02-19-2012 5:43 AM


How Does it Work?
Hi Genomicus and welcome to EvC Forum!

So, I have a couple of questions;

How does this front-loading work? What is the mechanism?

Can you show me an example of front-loading in a genome?

Are there front-loaded genes that exist now? How would we tell?

How would we differentiate between an organism whose gene had been front-loaded and one that had merely evolved?

Mutate and Survive


This message is a reply to:
 Message 1 by Genomicus, posted 02-19-2012 5:43 AM Genomicus has replied

Replies to this message:
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Genomicus
Member (Idle past 1261 days)
Posts: 852
Joined: 02-15-2012


Message 22 of 216 (653261)
02-19-2012 3:44 PM
Reply to: Message 20 by jar
02-19-2012 2:59 PM


Re: more just plain incorrect assertions.
quote:
That is simply not a prediction, just word salad. It is no different than saying the puddle was shaped to hold the water. It is just a nonsense assertion.

You have yet to back up your statement that it is no different than saying the puddle was shaped to hold water. How is it no different?

quote:
If you actually had read Stephen Freeland's work you would know that he has said 'that despite the continuing and widespread use of the phrase "universal genetic code", no such thing exists.'

That's because there are secondarily derived genetic codes. That's why in my essay I said the "nearly universal genetic code." There is indeed a nearly universal optimized genetic code. Some ciliates and other taxa use secondarily derived genetic codes. But the optimized genetic code is basal, and there is no indication it is derived. How do you account for this?

quote:
Not only is there no such thing as a universal genetic code, there is no indication that any genetic code is 'optimal' other then within the confines of that particular incident...

Other than within the confines of that particular incident? What incident are you speaking of? The work of Freeland et al. show that the canonical genetic code is highly optimized for error minimization. Why is there no phylogenetic tree consisting of sub-optimal codes in basal lineages, gradually leading to more optimal codes? What do you think is the best explanation for this phenomenon?


This message is a reply to:
 Message 20 by jar, posted 02-19-2012 2:59 PM jar has replied

Replies to this message:
 Message 24 by jar, posted 02-19-2012 4:08 PM Genomicus has replied
 Message 27 by Dr Jack, posted 02-19-2012 4:21 PM Genomicus has replied

  
Dr Jack
Member (Idle past 1424 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 23 of 216 (653263)
02-19-2012 4:07 PM
Reply to: Message 1 by Genomicus
02-19-2012 5:43 AM


Hello Genomicus,

Welcome to EvC

The front-loading hypothesis is an ID hypothesis that builds on Crick and Orgel’s directed panspermia hypothesis. In 1973, in a paper published in Icarus (“Directed Panspermia”), Crick and Orgel proposed that the earth was intentionally seeded with unicellular life forms.

I would note that Crick and Orgel have since rejected their views expressed in the 1973 paper as overly pessimistic - see Anticipating an RNA World.

1) The front-loading hypothesis predicts that the first genomes encoded genes that would be unnecessary (but beneficial) to early life forms, but necessary to the appearance of multicellular life forms and plants and animals. It predicts that the first organisms were not proto-cells, but highly advanced cells capable of terra-forming a hostile planet and able to shape future evolution in biased trajectories.

How do you intend to test this hypothesis?

2) The front-loading hypothesis predicts that prokaryotic homologs of important eukaryotic/metazoan proteins will be more highly conserved in sequence identity than the average prokaryotic protein.

The trouble with this prediction is that it does not, in fact, differ from the predictions of conventional theory. If a protein exists with homologes in Bacteria, Archaea and Eukarya* then it must have be strongly conserved, otherwise it wouldn't exist in all three domains. Such strongly conserved proteins will trivially be more highly conserved in sequence identity than other proteins.

This prediction makes sense from a rational design perspective because designing these prokaryotic homologs with functions that conserve their sequence identity will ensure that their 3D shapes will not be significantly changed by the blind watchmaker, preventing the appearance of eukaryotes (I realize that this prediction might sound a bit confusing – it’s past midnight where I am – so I’d be more than willing to elaborate on this).

Interestingly, the 3D shape of proteins is much more highly conserved than sequence identity. I'm not really sure how your justification follows, either.

* - It seems to me that Bacteria and Archaea are sufficiently distinct that they should be separately addressed in this kind of deep time discussion.

Edited by Mr Jack, : No reason given.


This message is a reply to:
 Message 1 by Genomicus, posted 02-19-2012 5:43 AM Genomicus has replied

Replies to this message:
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jar
Member
Posts: 33957
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.0


(1)
Message 24 of 216 (653264)
02-19-2012 4:08 PM
Reply to: Message 22 by Genomicus
02-19-2012 3:44 PM


Re: more just plain incorrect assertions.
Is it that you can't read or that you refuse to read?

You did read that the very source you are using says that there is no universal genetic code?

And that particular incident refers to any particular incident you select, just as every puddle is optimized for the water it holds and the water it holds is optimally designed to fit the puddle it's in.

Your use of the term 'optimal' is just word salad, nonsense; as absurd as all of the Intelligent Design crap.


Anyone so limited that they can only spell a word one way is severely handicapped!

This message is a reply to:
 Message 22 by Genomicus, posted 02-19-2012 3:44 PM Genomicus has replied

Replies to this message:
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Genomicus
Member (Idle past 1261 days)
Posts: 852
Joined: 02-15-2012


Message 25 of 216 (653265)
02-19-2012 4:10 PM
Reply to: Message 21 by Granny Magda
02-19-2012 3:02 PM


Re: How Does it Work?
quote:
Hi Genomicus and welcome to EvC Forum!

Thanks!

quote:
How does this front-loading work? What is the mechanism?

There are several mechanisms that could potentially be used. For example, if we wanted to front-load molecular machine X, we could design molecular machine Y into the first genomes. Molecular machine Y would have molecular machine X embedded within it. Further, molecular machine Y would be more complex (i.e., having more components) than molecular machine X. Subsequent deletion of several components in molecular machine Y would unveil molecular machine X. Possibly, we might have a real example of this in the biological world. Within the bacterial flagellum, an export system seems to be embedded. Deletion of the cap and hook proteins, and the motor proteins, would result in a protein export system that could mediate interactions between prokaryotes and eukaryotes.

Another way to front-load a biological system would be simply to make the appearance of that biological system much more probable. Suppose we wanted to front-load blood. In this case, we would endow the first life forms with homologs of hemoglobin, which would carry out an important function so that they don't decay over time as a result of natural selection and genetic drift. So, if the first life forms had homologs of hemoglobin, the blind watchmaker wouldn't have to tinker around, eventually happening to "land" on hemoglobin. The homologs of hemoglobin would already be in place.

quote:
Can you show me an example of front-loading in a genome?

By this do you mean an example of a genome that was front-loaded?

quote:
Are there front-loaded genes that exist now? How would we tell?

According to the front-loading hypothesis, genes that are important to multicellular life were front-loaded. Thus, Pax-6 genes, which are important in developmental pathways, would have been front-loaded from homologs in bacteria. Genes for brain development and brain function would be front-loaded. Blood would be front-loaded, if we're front-loading animals. How can we tell? In the first place, deep homology of these genes with prokaryotic genes would be indicative that they were front-loaded; if these prokaryotic homologs were fairly well-conserved in sequence identity, this would strengthen the hypothesis of front-loading further.

quote:
How would we differentiate between an organism whose gene had been front-loaded and one that had merely evolved?

You'd have to look at the broad biological context of the gene; determine its prokaryotic homolog and check their level of sequence conservation.


This message is a reply to:
 Message 21 by Granny Magda, posted 02-19-2012 3:02 PM Granny Magda has replied

Replies to this message:
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Genomicus
Member (Idle past 1261 days)
Posts: 852
Joined: 02-15-2012


Message 26 of 216 (653266)
02-19-2012 4:16 PM
Reply to: Message 24 by jar
02-19-2012 4:08 PM


Re: more just plain incorrect assertions.
quote:
You did read that the very source you are using says that there is no universal genetic code?

There is no truly universal genetic code. There is, however, a nearly universal genetic code, which happens to be highly optimized. How do you account for this?

quote:
And that particular incident refers to any particular incident you select, just as every puddle is optimized for the water it holds and the water it holds is optimally designed to fit the puddle it's in.

I really have no idea where you're going with "incidents" or what you mean by "incidents." The nearly universal genetic code is highly optimized for error minimization, as supported by the scientific literature. Do you think they've messed up badly?

quote:
...just as every puddle is optimized for the water it holds and the water it holds is optimally designed to fit the puddle it's in.

The analogy is entirely irrelevant, I'm afraid. Water fits into puddles "optimally" as a result of natural laws. Water flows downhill; thus, if water is flowing along, and a hole is in its path, it will fill up the hole as a result of gravity. It will fit the shape of the hole as a result of the chemical properties of the water. Things are different for the genetic code. There are no natural/chemical/physical laws that say that it must be optimal. The analogy does not hold.

Edited by Genomicus, : No reason given.


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 Message 24 by jar, posted 02-19-2012 4:08 PM jar has replied

Replies to this message:
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Dr Jack
Member (Idle past 1424 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


(1)
Message 27 of 216 (653267)
02-19-2012 4:21 PM
Reply to: Message 22 by Genomicus
02-19-2012 3:44 PM


Re: more just plain incorrect assertions.
Other than within the confines of that particular incident? What incident are you speaking of? The work of Freeland et al. show that the canonical genetic code is highly optimized for error minimization. Why is there no phylogenetic tree consisting of sub-optimal codes in basal lineages, gradually leading to more optimal codes? What do you think is the best explanation for this phenomenon?

Because the selective advantage of a high quality genetic code is high, and the nature of horizontal gene transfer means that there is an advantage in a shared genetic code.

Living prokaryotes are not ancient throwbacks, they do not represent the vestiges of an ancient world - they are extremely highly evolved organisms.


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jar
Member
Posts: 33957
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.0


Message 28 of 216 (653268)
02-19-2012 4:22 PM
Reply to: Message 26 by Genomicus
02-19-2012 4:16 PM


Re: more just plain incorrect assertions.
Okay, so we now know that you admit that there is no universal genetic code.

Now let's try to deal with your optimized bullshit.

What makes you think the genetic code is any more optimized than the water is to fill the puddle or the puddle is to fit the water?


Anyone so limited that they can only spell a word one way is severely handicapped!

This message is a reply to:
 Message 26 by Genomicus, posted 02-19-2012 4:16 PM Genomicus has replied

Replies to this message:
 Message 34 by Genomicus, posted 02-19-2012 5:01 PM jar has replied

  
DWIII
Member (Idle past 1072 days)
Posts: 72
From: United States
Joined: 06-30-2011


Message 29 of 216 (653269)
02-19-2012 4:37 PM
Reply to: Message 1 by Genomicus
02-19-2012 5:43 AM


Some objections...
Genomicus writes:


The front-loading hypothesis proposes that (a) early in earth’s history, the earth (or the solar system) was intentionally seeded with unicellular life forms (i.e., directed panspermia) and (b) these life forms contained the necessary genomic information to shape future evolution, such that the “course” of evolution was biased in pre-determined trajectories. Thus, evolution would be biased by the genomic information designed into the first genomes on our planet. There is evidence for the notion of panspermia, which I will discuss briefly. A “genomic clock” based on increases in genome sizes throughout the history of life on earth suggests that life may be roughly 10 billion years old (Sharov, 2006), which would indicate that the first organisms from which all present taxa descended did not originate on earth.

Panspermia, of course, pushes the problem one level deeper. Would it necessarily follow that the propagators themselves (of which you talk of) originated by way of earlier directed panspermiatic projects? Where does the chain end, if it ever ends?


Front-loading does not propose that all aspects of evolution were programmed and determined. There would be nothing stopping the blind watchmaker from taking its own unplanned courses alongside the front-loaded objectives. What might these objectives be? To use front-loading as a working hypothesis, it is assumed that multicellularity was an objective of the front-loading designers, as well as the origin of animals and plants. Further, the front-loading hypothesis proposes that the designers were rational agents; thus, poor, sloppy design in a biological system would count against the thesis that that system was designed into the first genomes.

And what's so special about multicellularity, then? The vast bulk (by mass) of life on Earth has been, and currently remains, unicellular (bacteria in particular). If multicellularity (and therefore plants and animals and fungi) was a legitimate goal, why not have started off with it immediately?


The genetic code is highly optimized for error minimization (Freeland et al., 2000). This optimal genetic code is nearly universal across all taxa. Curiously, there is no phylogenetic tree consisting of less optimal codes present in basal lineages, with more optimal codes being in late-branching taxa. This is interesting because if the genetic code evolved gradually, starting with less optimal codes (there are far more sub-optimal codes than there are optimal codes) which were gradually fine-tuned to produce the universal optimal code, we might expect such a phylogenetic tree to exist. Arguing that the sub-optimal codes once did exist early in life’s history, but vanished once the optimal codes came on the scene (i.e., that they were outcompeted), looks awfully ad hoc.

Unfortunately, constructing phylogenic trees requires the existence of intact genetic material, which by and large is not preserved over billions of years; and thus is necessarily limited to currently-living species.


Significantly, the fact that less optimal genetic codes do exist in nature (see Freeland et al., 2000; note that these sub-optimal codes are secondarily derived – that is, they evolved from the canonical genetic code, not the other way around) is proof-of-concept that the universal optimal code can exist without causing less optimal codes to vanish from the scene. The below image illustrates a hypothetical phylogenetic tree consisting of less optimal genetic codes in deep-branching lineages. It exemplifies what could have been the case, with different codes evolving into more optimal codes.

That the various extant alternative genetic codes are derivative from the "universal" code is quite uncontroversial, given that they seem more likely to have arisen via extreme genetic bottlenecks. Unfortunately, this says little to nothing about the actual origins of the universal code itself, except that it shows that even something as hard-wired as the universal genetic code is subject to a possibility of some change under the right circumstances. It is probably reasonable to infer that all known extant life forms one clade with its last common ancestor having had that particular code, but it does not preclude the past existence of other contemporaneous (and currently extinct) clades which had competing codes.


DWIII

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Granny Magda
Member (Idle past 154 days)
Posts: 2384
From: UK
Joined: 11-12-2007


Message 30 of 216 (653270)
02-19-2012 4:40 PM
Reply to: Message 25 by Genomicus
02-19-2012 4:10 PM


Re: How Does it Work?
For example, if we wanted to front-load molecular machine X, we could design molecular machine Y into the first genomes.

Merely using the phrase "molecular machine" does nothing to establish a mechanism. It is clearly a place-holder term that is standing in for an actual specific mechanism.

Am I to assume that you are doing this because you cannot name a specific mechanism?

Subsequent deletion of several components in molecular machine Y would unveil molecular machine X.

How exactly is that supposed to be achieved? How does the genome "know" which elements are to be deleted and which are to be retained?

Possibly, we might have a real example of this in the biological world. Within the bacterial flagellum, an export system seems to be embedded. Deletion of the cap and hook proteins, and the motor proteins, would result in a protein export system that could mediate interactions between prokaryotes and eukaryotes.

The problem with this is that it sounds very much like an evolutionary origin for the flagellum. It sounds like it would be equally compatible with the regular Theory of evolution.

Another way to front-load a biological system would be simply to make the appearance of that biological system much more probable. Suppose we wanted to front-load blood. In this case, we would endow the first life forms with homologs of hemoglobin, which would carry out an important function so that they don't decay over time as a result of natural selection and genetic drift. So, if the first life forms had homologs of hemoglobin, the blind watchmaker wouldn't have to tinker around, eventually happening to "land" on hemoglobin. The homologs of hemoglobin would already be in place.

So to follow on from that, can you show me that any such example has indeed occurred? Can you show me a front-loaded gene that has been taken up? And can explain how you differentiate it form one that merely evolved?

By this do you mean an example of a genome that was front-loaded?

No, I mean a gene that has been front-loaded but has not yet been, shall we say, "activated"? In other words, can you show me any allele that has been front-loaded but is not yet actively expressed in any extant organism?

According to the front-loading hypothesis, genes that are important to multicellular life were front-loaded. Thus, Pax-6 genes, which are important in developmental pathways, would have been front-loaded from homologs in bacteria.

Why choose multi-cellular life? It seems a bit random, was it picked out of a hat? Why not hypothesise that life was front-loaded to produce Archaea? Or bacteria?

Of course, I might hazard a guess. It's because the organisms that ID lobbyists really want to think have been front-loaded are humans. Because we're special. After all, Jesus does love us...

How can we tell? In the first place, deep homology of these genes with prokaryotic genes would be indicative that they were front-loaded;

Once again, this is indistinguishable from the consensus ToE, where the common ancestry of leads to homologous genes. In fact, a shared evolutionary heritage is pretty much part of the definition of a homologous gene. This seems to be another instance of this idea being unfalsifiable.
Are you saying that it is impossible for a non-front-loaded sequence to be highly conserved? I don't think it is.

So given that independently evolved sequences can be just as highly conserved, I fail to see how this can differentiate evolved systems form front-loaded ones.

You'd have to look at the broad biological context of the gene; determine its prokaryotic homolog and check their level of sequence conservation.

But again, that tells us nothing. It only tells us that the sequence is highly conserved. It does not tell us whether the conservation is due to front-loading or whether it is due to it simply being a useful and thus evolutionarily successful sequence.

It sounds to me like your hypothesis is lacking an actual mechanism, is based upon circular logic and assuming the consequent. It also smells, more than a little, of a convoluted Christian apologetic, wherein humans are the result of front-loading by the Christian god.

Mutate and Survive

Edited by Granny Magda, : No reason given.


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