The Scientific Method & Macroevolution?

lewiscalledhimmaster said:

Okay this may work for you as a scientist, but simplifying or turning stuff into metaphors might help some folks but I'm after the actual science involved.
Thanks nonetheless for the effort, but let's do some actual science please?

Thanks in advance.
lewiscalledhimmaster.

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What do you want to know about mutation?

lewiscalledhimmaster said:

Lay it on me! Everything you know.

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Not unless you pay me, and I don't come cheap. Pick a topic: kinds of mutation, causes of mutation, "randomness" of mutations, evolution of mutation rates, measurement of mutation rates, hypermutation. (No guarantee I'll answer, of course, but someone probably will.)

lewiscalledhimmaster said:

If that's the case, well a few crumbs off the table will be fine by me.

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I can lay out some of the basics.

1. Mutation rates vary between species, but remain relatively constant within species. For humans, each individual has roughly 60 mutations that they didn't inheret from their parents, and for the most part, they are either on noncoding DNA sequences or are just neutral mutations that do change the sequence of a gene, but not in a way that impacts function. Additionally, certain genes are more prone to mutation due to their location on chromosomes (certain regions are less stable and more exposed). Therefore, while mutations are often discussed as being "random", they do have patterns and can be predicted to a degree, so they aren't truly random.

2. Mutations can occur in any sort of cell that replicates its DNA at any point in one's life, but they aren't passed down unless they occur in reproductive cells. Environmental factors such as radiation, certain chemicals, and even stress can increase mutation rates and hinder the natural DNA repair our cells perform to prevent a buildup of mutations. However, even in ideal conditions, DNA replication is an imperfect process that inevitably results in mutations.

3. Mutations can have both positive and negative effects, with one of the most striking examples being a disabled gene in humans that regulates brain growth. It allows our brains to develop more and faster than, say, a chimpanzee, but it also increases the risk of brain cancers. As it turns out, intelligence is more beneficial to survival than this cancer risk is a detriment to it.

lewiscalledhimmaster said:

Let's just say you decide to answer, how about starting with the first one: kinds of mutation?

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Substitution: One base of DNA ends up being replaced with another, with effects ranging from absolutely nothing to certain diseases such as sickle cell anemia or terminal illness if it alters a vitally important gene.

Deletion: a portion of DNA becomes lost, leaving out as little as a single base to as much as a visible portion of a chromosome.

Insertion: extra bases are added.

When a deletion or an insertion impacts how the DNA strand is "read", it is considered to be a frameshift mutation. This usually results in highly altered protein production, and for this reason the impact of deletions and insertions tends to be bigger than the impact of substitutions.

I took this upon myself since I am on and the material is pretty basic.

Here are ones where the changes become more specific.

Nonsense mutation: makes a stop codon in an inappropriate place, which signals the end of protein coding.

Missense: Changes the coding for an amino acid to a different one.

Silent: changes a base, but thanks to many proteins being coded for by a number of different sequences, the protein coded for remains the same.

PsychoSarah said:

Substitution: One base of DNA ends up being replaced with another, with effects ranging from absolutely nothing to certain diseases such as sickle cell anemia or terminal illness if it alters a vitally important gene.

Deletion: a portion of DNA becomes lost, leaving out as little as a single base to as much as a visible portion of a chromosome.

Insertion: extra bases are added.

When a deletion or an insertion impacts how the DNA strand is "read", it is considered to be a frameshift mutation. This usually results in highly altered protein production, and for this reason the impact of deletions and insertions tends to be bigger than the impact of substitutions.

I took this upon myself since I am on and the material is pretty basic.

Here are ones where the changes become more specific.

Nonsense mutation: makes a stop codon in an inappropriate place, which signals the end of protein coding.

Missense: Changes the coding for an amino acid to a different one.

Silent: changes a base, but thanks to many proteins being coded for by a number of different sequences, the protein coded for remains the same.

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Note that frameshift, nonsense, missense and silent are categories that apply only to DNA that codes for proteins. That's critical DNA, but it only accounts for about 2% of the genome, and maybe 20% of functional DNA.

Other details:

Substitutions often occur during replication, when the wrong base can simply be inserted. DNA polymerases (the enzymes that copy DNA) often have proof-reading capability, but it is not infallible. Chemically similar bases are more likely to be incorporated by mistake than chemically different bases; A and G are chemically similar, as are C and T, so mutation within each pair is more likely than between pairs.

Insertions and deletions are collectively called "indels", because it's often impossible to say which has occurred: on sequence has DNA that the other lacks, but you can't tell just by comparing them whether DNA was inserted into one or deleted from the other.

Some indels happen very frequently. When short stretches of DNA are repeated multiple times in a row (e.g. AGTAGTAGTAGT), it's called a short tandem repeat or microsatellite, and these tend to be quite unstable, with the number of copies changing up or down frequently.

Chunks of DNA can also be inserted backwards; this is known as an inversion. Large (> ~1000 bases) indels and inversions are collectively known as structural variation.

whois said:

the "method" isn't exact in theory or practice.
it's a method of discovery, and you use it more than you can imagine.
it's a natural outgrowth of mans desire to know.

apparently it means the result of accumulating changes, over the course of an indefinite time.
apparently, some species never "evolve".

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Technically, no species evolve. ''Species'' is a part of the taxonomic classification, which is itself a kind of codification system for organisms that humans ascribe to distinguish between organisms with particular physical characteristics. If a certain organism classified within a species evolves different characteristics then it ceases to be a member of that species.

A lot of the arguments I hear are actually semantic misunderstandings, usually in ignorance of the distinction between ''organism'' and ''species''.

Creationists tend to talk about ''speciation''. Scientists call this ''diversification''. There is a reason for that.

When we talk about the diversification of life, we're talking about how the evolutionary tree widens with time and new ''species'' come to be. I imagine this puts in mind, for creationists, new species popping out of thin air, or an ape waking up as a giraffe or something. What actually happens is that mutations in species are either advantageous or they are not and they dictate the directions organisms evolve (or don't evolve).

If an organism gets a mutation that gives it very small muscles, then it is weak, it does not get much of a chance to procreate and pass on that mutation. It may even die before it gets that chance. If an organism gets a mutation that gives them larger muscle mass and makes them stronger then they have more chance of living, thus procreating and passing on that mutation.

Further down that organism's lineage, other mutations happen and they accumulate in the lineage until these mutations have caused this organism to be sufficiently different in its physical characteristics from its ancestry to be considered a new species. But be aware, we, humans are the ones who classify it as such. It is not objectively an entirely separate kind of organism from its ancestry. It is just different enough, through cumulative mutation, that we classify it as a different species.

Creationists will say ''ha, it's a new species, and we've never witnessed anything becoming a new species'', without realizing that we only classify things as new species when they are sufficiently different form their ancestry to be considered so. It's an arbitrary classification system (though with many recent standardizations). What if we were to, arbitrarily, decide that one single genetic difference is enough to classify something as a new species? Then every single organism on Earth would be a separate species, because no two organisms (other than identical twins) share exactly the same genetics.

This is why ''speciation'' is a bad term. It assumes organisms as objectively separate from one another and then forms the opinion that they don't mix, or that one can't come form another. This is also patently false.

If we look at the fossil record, we can see that at the deepest strata, there are few forms of life, and as we get closer to the surface of the Earth, life diversifies. It is a bottom up ''tree of evolution''.

I would challenge any creationist to tell me why, as we go up the strata which have deposited material over billions of years, life gets more diverse as time goes on. If there were only a few species at the deepest layers, yet millions at the shallowest layers -- bearing in mind that species are organisms with different physical characteristics from others -- how did those millions of physically different organisms come to be if not by evolution of their physical characteristics?

Is it a case of ''God planted them there to confuse us''? You see, there's no logical explanation for the diversification of life other than evolution.

Mediate said:

Technically, no species evolve. ''Species'' is a part of the taxonomic classification, which is itself a kind of codification system for organisms that humans ascribe to distinguish between organisms with particular physical characteristics. If a certain organism classified within a species evolves different characteristics then it ceases to be a member of that species.

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No, that's not right. There can be plenty of evolution within a species. Species as a category can be defined either as a potentially interbreeding population, or by physical characteristics, but in either case the genetic and phenotypic composition of the population can change.

Creationists tend to talk about ''speciation''. Scientists call this ''diversification''. There is a reason for that.

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No, scientists call it speciation. See, for example, Coyne and Orr's book on speciation, called Speciation.

This is why ''speciation'' is a bad term. It assumes organisms as objectively separate from one another and then forms the opinion that they don't mix, or that one can't come form another. This is also patently false.

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Species as defined by the biological species concept (in one form or another) are indeed objective entities, even if the boundaries are sometimes fuzzy.

sfs said:

There can be plenty of evolution within a species.

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And if it were to "flood the market," so to speak, then they just take it out of the system and place it in a new category ... correct?

Such as bacteria, which I believe creates a new species every nine hours.

But that would result in such a flood of Linnaen paperwork, it wouldn't be cost effective to try and keep up.

So simply take bacteria out of the mainline and put it in a category all by itself.

(Only on paper.)

sfs said:

No, that's not right. There can be plenty of evolution within a species. Species as a category can be defined either as a potentially interbreeding population, or by physical characteristics, but in either case the genetic and phenotypic composition of the population can change.


No, scientists call it speciation. See, for example, Coyne and Orr's book on speciation, called Speciation.


Species as defined by the biological species concept (in one form or another) are indeed objective entities, even if the boundaries are sometimes fuzzy.

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The point is species are arbitrarily defined by humans, insofar as taxonomy is a classification whose boundaries we decide upon. The other point is, the argument against evolution ''a certain organism can't evolve into another one/we haven't witnessed it/''macroevolution'' or ''speciation'' is not possible/dogs don't turn into cats'' is faulty because it fails to acknowledge (in most cases that I've seen) that species are arbitrary definitions and that organisms would evolve and change independent of whichever boxes we ascribe to those changes. Our boxing of one species as separate from another doesn't stop an organism classified as a certain species from mutating, or one day, being sufficiently different that we classify it as some other species entirely.

Obviously a species can change in its gene pool or have slightly different characteristics and still remain part of its species. What I should have said was ''specific species don't evolve beyond their species and still get to remain in the same species bracket''. That might seem obvious, but it has implications in this argument because a lot of creationists seem to discount evolution because species (by their very classifications) are separated in this way. Creationists often make the argument that a dog doesn't evolve into a cat and this is thought of as a fair argument by them because they don't understand that we classify these as separate species for a reason. They can't breed with one another because they diverged at certain points and developed characteristics that now mean they cannot converge in their current physical states. That separateness and incompatibility seems to be to creationists evidence that evolution is false.

That's where the Ken-Ham-esque argument comes from that ''microevolution exists'' but ''macroevolution doesn't'' and things are either ''one kind'' or ''another kind'' because they were all created on the same week. It's a fundamental misunderstanding of the fact that organisms' classifications are arbitrary in that they are ascribed by humans, not by the cosmic laws of nature. Nature doesn't classify species, we do, and the logical lead-on from that is that we could classify species on a much narrower frame and everything would be a separate species, because every organism has slightly different DNA.

Obviously that would be silly, but the idea serves to illustrate that in fact, just because there's a difference in physical characteristics doesn't make a ''species'' evolutionarily unconnected to another ''species'', which is the assumption that underpins that Ken-Hammish argument.

Seems like I'm saying the same thing in a lot of different ways but that's because I find it hard to put into words that actually illustrate the argument, because a lot of what I'm saying seems common sense but when you really get into it their is a fundamental common-sense discrepancy between creationists and evolutionists.

It seems to me, on some level, that evolutionists recognize that evolution is an ongoing, neverending process when it comes to life on Earth, where creationists seem to think it impossible that fish ever evolved throughout the ages to give rise to amphibians. In the creationists mind, they are separate, totally unconnected things.

AV1611VET said:

And if it were to "flood the market," so to speak, then they just take it out of the system and place it in a new category ... correct?

Such as bacteria, which I believe creates a new species every nine hours.

But that would result in such a flood of Linnaen paperwork, it wouldn't be cost effective to try and keep up.

So simply take bacteria out of the mainline and put it in a category all by itself.

(Only on paper.)

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9 hours might be the generation time for some bacteria. but, yeah, new species might pop up on a yearly basis if not faster. organisms that reproduce faster evolve faster, generally speaking.

Mediate said:

Technically, no species evolve.

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let's not cloud the issue shall we.
question:
if "species" do not evolve, how does diversification happen?
it's either the "spontaneous generation" or the accumulating changes.

''Species'' is a part of the taxonomic classification, which is itself a kind of codification system for organisms that humans ascribe to distinguish between organisms with particular physical characteristics. If a certain organism classified within a species evolves different characteristics then it ceases to be a member of that species.

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yes, i heard all about this.

A lot of the arguments I hear are actually semantic misunderstandings, usually in ignorance of the distinction between ''organism'' and ''species''.

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organism, a symbolic representation of any and all life.
species, a specific kind of organism.
what's so hard about that?

When we talk about the diversification of life, we're talking about how the evolutionary tree widens with time and new ''species'' come to be.

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this is an assumption.
it's a good, reasonable guess, but that's all it is.

I imagine this puts in mind, for creationists, new species popping out of thin air, or an ape waking up as a giraffe or something.

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i believe you would be wrong.

What actually happens is that mutations in species are either advantageous or they are not and they dictate the directions organisms evolve (or don't evolve).

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yes, it would be reasonable to assume such a thing.

Is it a case of ''God planted them there to confuse us''? You see, there's no logical explanation for the diversification of life other than evolution.

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it's really hard to choose which absurdity:
there is a god, or things becoming alive.
please, don't start with the abiogenesis bit.

You see, there's no logical explanation for the diversification of life other than evolution.

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Quite literally, the definition of proven beyond a reasonable doubt.

crjmurray said:

Quite literally, the definition of proven beyond a reasonable doubt.

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evolution is far from being proven.
it seems to be making progress though.

whois said:

evolution is far from being proven.
it seems to be making progress though.

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Oh is there a logical alternative?

Bacteria evolve into.....bacteria?

justlookinla said:

Bacteria evolve into.....bacteria?

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Pardon?