The Neutral Theory of Evolution


(Ann Gauger) #66

I thought it was more like Lewis Carroll myself.

Koonin is a great scientist and I respect him highly, but his belief in the power of exaptation rests on no evidence, merely an appearance of evidence and a desire for explanation. I know Lynch’s work, and he is correct, selection is weak and cannot remove near neutral mutations, so one can expect the accumulation of repetitive elements, pseudogenes etc. But there is no reason to expect such accumulation to lead to functionality, let alone increasing complexity, unless the process has been guided.


(Joseph Akins) #67

Things certainly do get curiouser and curiouser the deeper we go.

Lynch and Koonin seem to appeal to Constructive Neutral Evolution, but this seems to be more of a counter to IC than a thorough explanation. But, I must admit that I have not read much on it.


(Blogging Graduate Student) #68

Guided… By selection. Koonin and Lynch propose a neutral accumulation of substrates for later evolution towards function via natural selection.


(Ann Gauger) #69

I’ll have to have this discussion later.


(Bill Cole) #70

Exactly. The only thing we should expect is sequence degradation.


(Jon Garvey) #71

Koonin, at least, appears to equate “complexity” (which neutral theory explains) with “creativity” (which it doesn’t). Tangled string is complex, but I want to know about peregrine falcons and giraffes.


(Joseph Akins) #72

You’re appealing to an invisible hand. Natural selection is only a filter. For instance, tour guides only have a job if they’ve been to, or know of, the sites visited beforehand. I don’t think that is the point you wish to make about natural selection is it? But, your answer has made my point at least in the sense that unfiltered by computer algorithms our everyday experiences guide us to speak of evolution in teleological terms even at the molecular level. Why?


(Blogging Graduate Student) #73

Of course natural selection is only a filter. That’s precisely why throwing more substrate at it would lead to a greater diversity of adaptations. We often fall into using teleological terms because these are more intuitive for us as telological agents to understand. Are you suggesting that it actually hints towards something more profound?


(Joseph Akins) #74

Yes, that the production of substrates must be controlled somehow.

I don’t find “throwing more substrate at it” a viable option. To extend the filter analogy perhaps too far: What happens to a filter when too much material is passing through it? The system gets gummed up. In this case it would be the cells themselves.

Neutral theory exists because Natural Selection of beneficial mutations cannot explain naturalistic evolution; too many “just so” positive mutations are required. You seem to be saying neutral molecular evolution provides so many combinations of substrate that purifying selection can filter out the detrimental ones and allow the neutral and adaptive “just so” combinations to pass. Without forecasting future environmental changes how do all of these substrates not gum up cellular processes? Why would the cell waste energy/resources doing it? That is why I do think it is a guided process and operates within preset boundaries.

In some sense this is why eukaryotes have a nucleus.


(George) #75

@agauger,

Please note the wording if your sentence I celebrate above!!!

In this case, I hope my reputation for one thing precedes me! For more than a year, I have been the BioLogis participant MOST LIKELY to serve up a daily mantra that Christians SHOULD hold to Evolution as a God-Guided process!

I didn’t do it to shake up folks… I did it so folks would get increasingly comfortable discussing the ramifications… rather than ducking the words!

And I will continue to argue FOR the specific point.

The only difference between my view and the view of some evangelicals is this: I do not believe science can prove God’s Guidance… short of God coding mitochondrial DNA to record the words to John 3:16 in 16 bit digital Greek form!


(Blogging Graduate Student) #76

The fact that we often slip into teleological language hints that the production of substrates must be controlled? I don’t think that follows at all.

It’s not that the system gets “gummed up” in the sense that it starts to have problems, it’s that there would be an accumulation of neutral sequences that natural selection wouldn’t have managed to purge. That’s exactly what we see in complex organisms - accumulation of neutral sequences.

I don’t understand this objection. Why would forecasting the future be required? Neutral sequences by definition do not “gum up” cellular processes. Are you worried about the fitness cost of replicating all that excess DNA over many generations?


#77

That’s an incorrect conclusion, IMHO.

The sequence data reveals the rates by which mutations are fixed in populations. Neutral theory explains that the majority of these mutations are fixed by neutral drift, not selection, or carried along with selection non-specifically. It’s got nothing to do with whether evolution needs “too many positive mutations.”

It’s also not the be-all or end-all of evolutionary theories.


(George) #78

@EvolvableCreationist,

@Argon is right about you being wrong on this.

To a large extent, Neutral Theory exists as a corrective to the too common belief that Evolution has no strong correlation to swings in environmental factors. Mutations occur during long epochs of environmental constancy (allowing a build up of quiet genetic diversity) … and the high pitch of natural selection UNCOVERS this diversity when the environment suddenly swings one way or another!

One of the TRUTHS of human evolution was the changes in African jungles where forests began to open up into vast areas of grasslands… with human groups having to find food and water out in the predator-filled openess…and the changes to hominids that made this possible.

Chimpanzees, and even Gorillas, stayed mostly within reach of the safety in the trees… baboons came out into the grasslands… but followed a different genetic path that did not lead to hominids status.


(Joseph Akins) #79

@argon, @gbrooks9,
My view on the origin of Neutral Theory being due to the inability of beneficial mutations, though not well expressed, is based on my reading of Kimura’s 1968 Nature paper. Natural selection failed to explain the data, and he concluded given the number of mutations needed most must be neutral.

Kimura (1968) “ Actually, the calculation of the cost based on Haldane’s formula shows that if new alleles produced by nucleotide replacement are substituted in a population at the rate of one substitution every 2 yr, then the substitutional load becomes so large that no mammalian species could tolerate it.
Thus the very high rate of nucleotide substitution which I have calculated can only be reconciled with the limit set by the substitutional load by assuming that most mutations produced by nucleotide replacement are almost neutral in natural selection.”
http://www.blackwellpublishing.com/ridley/classictexts/kimura.pdf


(Joseph Akins) #80

What do you mean by this? I’m envisioning a cell gummed up by protein substrates just waiting around to be useful. That’s obviously not what you mean by this statement.

In your more recent response you say:

No, but throwing proteins at the filter of Natural Selection hoping some will be adaptive will inhibit cellular processes. I’m thinking more of tinkering that results in exaptations and MGE “being recruited”, as mentioned in my original post, not as much incremental neutral changes that make a protein advantageous in some future environment. I’m not worried about eye color, but how eukaryotes first developed a nucleus.


(Blogging Graduate Student) #81

For a start, the accumulation of neutral substrates does not just refer to the accumulation of random protein sequences in the cell. That’s part of it, but a relatively minor part. Most randomly produced proteins are short and disordered, so don’t interfere with the function of the cell significantly as they are quickly degraded by proteases. This is the neutral part. A much smaller proportion of these sequences (at any one time) will randomly gain functional domains, and then they can start to influence the cell, for better or worse - this is where the selection comes in. The point is that having a large amount of neutral substrate in the background increases the options that will be explored.

I’m confused, because those are 2 descriptions of the same thing. What’s “MGE”?


(Jon Garvey) #82

A lay analogy - the average attic or basement contains a lot of junk. Most of it never finds a use - or if it does, it’s because it had a use before it became junk. It would seem there has to be teleology in the sytem (the broadest definition of teleology, ie either that organisms “know” what might come in handy later, or that the molecular realities are biased towards useful stuff.

In other words, the basement appears to be full of old nuts and bolts rather than earth.


(Joseph Akins) #83

This is close to how I see evolution, however, the notion that the organism ”knows” how to put items in the attic to any use is troubling to me. My own view is that a third party has set the system up such that tinkering is biased to “useful stuff”. I’ll open this as a new thread at some point. Still trying to get a more intuitive understanding of Neutral Theory.


(Joseph Akins) #84

From my original post in this thread:

MGEs are transposing, retrotransposons, bacteriophages, plasmids, etc. For Koonin’s take on parasite-host interactions and MGEs up to the onset of multicellularity see Koonin (2016). As a virologist he has profound insight into this. http://rstb.royalsocietypublishing.org/content/371/1701/20150442

But, to paraphrase Jacob (1977) “On Evolution and Tinkering” the really creative parts of biochemistry occurred early in life’s history, big steps in evolution required new information and specialization and diversification are more a matter of regulation than structure.

I understand neutral molecular evolution as Kimura explained it in 1968; it’s the regulation and timing that are the issue.


(Jon Garvey) #85

I put the “know” in scare quotes to indicate that I wasn’t proposing conscious forward planning, but rather some kind of intrinsic teleology.

But I’d be interested to know exactly what you found troubling, because it was the desire to rid nature of “teleological powers” that caused the early modern scientists to insist matter is only inert particles, subject to the laws of God. Descartes, for that reason, considered animals to be mere automatons, and the non-physical human soul the only purposeful thing within nature.

In this way, God was the only source of direction in nature, acting externally through laws of nature.

Do we still think either animals, or nature, are that inert, and if so do we have good grounds for it? Neutral theory, as constituted, very much treats genetic material as changing nore or less entirely passively, and ends up (apparently) in magical thinking.