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Author Topic:   Extent of Mutational Capability
Taq
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Message 4 of 279 (793000)
10-18-2016 10:46 AM
Reply to: Message 1 by Gregory Rogers
10-18-2016 8:10 AM


Gregory Roberts writes:
Is there any known process or element in the genetic make-up of animal organisms, or else anything within biology, that would actively stop or act as a barrier to so-called 'macroevolution’.
As macroevolution is defined by science and observed in the fossil record, then no, there is no barrier to macroevolution.
The differences we see between the genomes of living species is consistent with the observed mutations that biological organisms naturally create. They include substitution, insertion, deletion, and recombination events. All life uses the same genetic and metabolic pathways.
What I would consider to be a barrier to macroevolution is if macroevolution required a complete rewrite of both genetics and metabolism, the foundational functions of any organism. For example, if chimps used a completely different codon table than humans, then I would say there is a very significant and very possibly an impenetrable barrier to macroevolution. As it is, we use the same codons, the same metabolic pathways, and only differ by 2 or 4% at the sequence level (depending on how you count insertions and deletions).
In other words, anything known to genetics that would prevent transformation or mutation from one animal category to another, i.e., any process that would preclude, for example, an ape-like form evolving into a human being, a dinosaur evolving into a bird, and so forth.
The problem with this argument is that apes, humans, dinosaurs, and birds are all in the same animal category. We are all amniotes. Nowhere in the historic evolution of animals do we require a completely new animal to evolve. Chimps and humans are both primates, as was our common ancestor. Bears and humans are both mammals, as was our common ancestor. Fish and humans are both vertebrates, as was our common ancestor.
However, the creationist counter-argument is, I believe, that DNA make-up is like a computer software programme, and that it cannot develop outside of its basic programming. Thus a cat could never evolve into a dog, etc.
If DNA can't be changed then how are both cats and dogs able to survive with different DNA sequences in their genomes? According to this creationist argument, there should only be one species, and every member of that species should have identical genomes. Obviously, this isn't the case.
DNA can change, and changes in DNA can lead to new species with new functions and new morphology. In fact, we do see DNA changing in real populations in real time.
Edited by Taq, : No reason given.

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 7 of 279 (793013)
10-18-2016 2:38 PM
Reply to: Message 5 by 1.61803
10-18-2016 11:40 AM


Re: From shrew to you
1.61803 writes:
In 1997 scientist discovered that whales are related to cows and hippos. That is about as counter intuitive as it gets imo.
Humans are also related to cows and hippos. All species are related to one another.

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 11 of 279 (793019)
10-18-2016 4:21 PM
Reply to: Message 9 by dwise1
10-18-2016 3:29 PM


Re: No Barriers to Macroevolution
dwise1 writes:
And don't even get us started on the "basic worm kind". That "simple" "baramin" is filled with reproductive barriers.
As I am sure you are aware, there are creationists who consider all birds to be a single created kind, hummingbird to ostrich.
What I find most curious about their position is the genetic comparisons. Creationists will often claim that the genetic differences between humans and chimps is a gulf that evolution can no cross. However, there are many species within a supposed created kind that have more genetic between them than do chimps and humans. In fact, there are more differences between any two ape species than there is between a chimp and human.

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


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Message 12 of 279 (793020)
10-18-2016 4:25 PM
Reply to: Message 10 by 1.61803
10-18-2016 3:30 PM


Re: From shrew to you
1.61803 writes:
My Haiku on common descent
I believe this to be true
all creatures are kin
How could it be otherwise
New flowers budding
Branch tips reaching up to sky
Phylogeny

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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 14 of 279 (793022)
10-18-2016 4:35 PM
Reply to: Message 13 by 1.61803
10-18-2016 4:32 PM


Re: From shrew to you
"Phylogeny"
I think you need 5 syllables there.
Its 5 syllables when I say it.

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


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Message 21 of 279 (793042)
10-19-2016 11:01 AM
Reply to: Message 18 by Diomedes
10-19-2016 9:33 AM


Re: Creation "science" again
Diomedes writes:
On a side bar, I HATE the usage of terms like microevolution and macroevolution. To me, there is only 'evolution'.
What we have is two groups who focus on two different things. Creationists are obsessed with using labels, and judging everything from those labels. Scientists are more interested in explaining how the natural world works, and could care less about the need to neatly pigeon hole observations into one term over another.
For scientists, they are interested in why species differ from each other. Their explanation, backed by evidence, is speciation followed by divergence. Scientists have come to use the term "macroevolution" as a label for this process.
Creationists, on the other hand, believe that if they their use of words somehow forces nature to conform to their beliefs. If they can call one thing macroevolution, then they believe that the mere utterance of the word macroevolution can somehow falsify any other explanation.
What we have is two different worldviews of how the map relates to the territory. Creationists believe that a continent will reshape itself to match what they draw on a map. Scientists believe that they should draw a map so that it matches what the actual continent looks like. Reasonable people can use their own judgment to determine which is the most logical approach.
Edited by Taq, : No reason given.

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 25 of 279 (793064)
10-19-2016 5:25 PM
Reply to: Message 23 by dwise1
10-19-2016 3:01 PM


Re: Creation "science" again
dwise1 writes:
A couple decades ago, a creationist on a different forum made me realize this basic truth about creationism: the fundamental purpose for everything that they do is convincing people.
I have been coming to creo v. evo forums for over a decade now, which is probably half the time you have spent in such forums. I think I remember you saying you were on pre-HTML forums at one point, if memory serves. Still, I have seen more than my fair share of the species Onlinae creationistii, so if I may offer my two cents (which could be completely wrong). . .
I don't think they are trying to convince non-creationists. I think creationists are only trying to convince themselves that they are justified in their beliefs. This conclusion is based on quite a few things, but there is one main pillar: Creationists prefer echo chambers. They refuse to learn actual science, refuse to engage the actual scientific community, and refuse to scientifically test their ideas. We can also point to the pervasive creationist claim that they are being persecuted, yet another justification for believing that they are right.
I don't want to get too far into the metadebate, so let's bring this back around to created kinds. The superficial nature of "created kinds" can only survive in an echo chamber where no one asks for a scientific or objective definition for created kinds. As soon as created kinds are questioned they fold in on themselves like a wet paper bag. Arguing for created kinds can't convince anyone who even starts to scratch at the surface of the argument. The only purpose of created kinds is to have a sciencey sounding justification for believing in creationism.
We can look at a specific example which may better illustrate the problem creationists have. I have asked this one simple question in many different forums over many years. I have yet to find a creationist who can answer the following question (in a way that supports creationism):
"What features would a fossil need in order for YOU to accept it as a transitional fossil between humans and an ancestor shared with chimps?"
The only honest answer I have ever received from creationists on this question is that no matter what a fossil looks like, they would never accept it as being transitional. A few honest creationists will admit that their position is completely dogmatic, but for the most part creationists will ignore that question.
Deep down, they know what would convince people: evidence. They know they don't have it. What they do have the ability to do is create an echo chamber where they aren't reminded of that fact.

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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 87 of 279 (793237)
10-24-2016 1:26 PM
Reply to: Message 73 by CRR
10-23-2016 4:53 PM


Re: What is a "kind"?
CRR writes:
I have provided a definition of kind as per Percy's request [#45] and in response to others. The definition I favour is "those animals/plants that could interbreed immediately following creation". You might not agree with it but you now have one.
I am more than happy to use this definition. If we define a kind as a group of species that share a common ancestor then all animals (and all sexually reproducing eukaryotes) are in the same kind. Problem solved. It is microevolution all the way back to the common ancestor of all sexually reproducing eukaryotes when we use your definition.
RAZD has also proposed a definition "A "kind" would then be a clade with no previous ancestor." I think this is workable so long as you suspend the inherent assumption of cladistics that all clades are subsets of the LUCA clade. (Please note that RAZD does not accept that such kinds actually exist.)
It isn't an assumption. It is a conclusion drawn from evidence. For example, the congruence of independent phylogenies is smoking gun evidence for shared ancestry:
29+ Evidences for Macroevolution: Part 1

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 88 of 279 (793238)
10-24-2016 1:28 PM
Reply to: Message 77 by Coyote
10-23-2016 11:21 PM


Coyote writes:
Any definition creationists come up with for "kind," which makes the "cat kind" and the "dog kind" come out the way they want, also makes the "ape kind" work as well, an idea which most of them absolutely reject!
Don't forget that the mammal kind works as well, which demonstrates that dogs, cats, and apes are all in the same kind.

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


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Message 89 of 279 (793239)
10-24-2016 1:33 PM
Reply to: Message 85 by Dr Adequate
10-24-2016 11:37 AM


Re: Proposition: Another Angle
Dr Adequate writes:
Now, given my previous post you may wonder how we are so sure that (to continue with my example) evolution from more basal apes to humans did take place. Well, we can look at the fossil record, and we can see lots of intermediate forms. And (see my first post on this thread) we can see that in no case in the transition can we say that mutation can't have achieved that (because, as I pointed out in my first post, mutation as such can do anything); nor can we say that natural selection would have prevented the transition, because all the intermediate forms look very plausible as intermediate forms.
We also have genome sequences for all the ape species (including humans). If apes (i.e. chimps, bonobos, gorillas, and orangutans) evolved from a single ancestor not shared with humans then we can predict what we should see from a genome comparison. What we should see is humans as an outgroup from the ape phylogeny. That isn't what we see. We see that humans are IN the ape phylogeny.
Comparative and demographic analysis of orang-utan genomes | Nature
Chimps share more DNA with humans than they do with gorillas and orangutans. This puts humans in the ape clade.
Edited by Taq, : No reason given.

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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 90 of 279 (793240)
10-24-2016 1:37 PM
Reply to: Message 39 by CRR
10-21-2016 2:16 AM


CRR writes:
Yes changes requiring multiple neutral mutations can happen such as chloroquinine resistance in malaria (due to a fault in a transport protein). This required only 2 neutral or near neutral mutations and took a long time to occur in a large population with short reproduction times. In small populations with long reproduction times, such as humans, the waiting time becomes prohibitive, especially when larger numbers of neutral mutations are required to get a benefit.
Until you can actually show that these barriers exist between two species, your are just whistling Dixie.
For example, of the differences between humans and chimps, how many are beneficial differences that required multiple neutral mutations? If you can't point to a single one, then you have no argument against evolution.

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 94 of 279 (793247)
10-24-2016 3:03 PM
Reply to: Message 92 by Dr Adequate
10-24-2016 2:33 PM


Re: Proposition: Another Angle
Dr Adequate writes:
Quite so. And one should emphasize that not only does that mean that humans are closer to chimps than they are to anything else (after all, we have to be closest to something) but also chimps are closer to humans than anything else (e.g. gorillas).
Here is the thing. We don't have to be closer to one species (as determined by statistical significance). As a lineage changes over time it does not become more like another lineage over time. If humans and apes had a separate common ancestor then humans should be diverging by the same amount as compared to all other ape species. What we should see is the same genetic distance between humans and all other ape species.
"The well-established genetic equidistance result shows that sister species are approximately equidistant to a simpler outgroup as measured by DNA or protein dissimilarity."
The Genetic Equidistance Result of Molecular Evolution is Independent of Mutation Rates - PMC
The only reason that humans should be more like one ape species than another is if humans share a more recent common ancestor with one ape species, as compared to all other ape species.
In the ape phylogeny illustrated in the previous post, the genetic distance between orangutans and gorillas is the same as the genetic distance between orangutans and humans. However, gorillas and humans are closer than gorillas and orangutans. It is this pattern of differences and equidistance that allows us to construct phylogenies and evidence shared ancestry.
It is actually fun to play around with genetic equidistance at Homologene. For example, we can look at cytochrome c:
HomoloGene - NCBI
If you click on the "Show Pairwise Alignment Scores" on the left hand side of the page, you get this comparison between model organisms:
HomoloGene - NCBI
For the DNA results you get:
Human v. Mouse: 90.5%
Human v. Chicken: 81.6%
Mouse v. Chicken: 81.9%
You get nearly the same distance between mouse and chicken as you see between human and chicken, exactly what you should see if evolution and common ancestry are true.
I
Edited by Taq, : No reason given.
Edited by Taq, : No reason given.

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Replies to this message:
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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 95 of 279 (793248)
10-24-2016 3:09 PM
Reply to: Message 91 by herebedragons
10-24-2016 2:10 PM


Re: Parentless Clades
herebedragons writes:
I have to correct you on this, RAZD; someone else also said something similar a few messages back, but it is not really correct. Cladistic analyses have three basic assumptions:
1. The groups being studied are related by descent from a common ancestor
2. The pattern of cladogenesis is bifurcating
3. Changes in character state occur in lineages over time
See: Introduction to Cladistics
A cladistic analysis will always create a bifurcating tree where all organism being studied are related. So cladistics does not test to determine IF they are related but rather HOW they are related. This cladogram is then the hypothesis as to how the organisms are related and possibly how a particular character has evolved.
That is simply false. Do you have to assume the defendant is guilty in order to do a DNA fingerprinting test? Of course not. Cladistics analysis is no different. If there are many trees supported by the data then you will get a low statistical score from cladistics methods. Only real common ancestry (or highly improbable chance processes) produces objective and statistically significant results when using these methods.
"The degree to which a given phylogeny displays a unique, well-supported, objective nested hierarchy can be rigorously quantified. Several different statistical tests have been developed for determining whether a phylogeny has a subjective or objective nested hierarchy, or whether a given nested hierarchy could have been generated by a chance process instead of a genealogical process (Swofford 1996, p. 504). These tests measure the degree of "cladistic hierarchical structure" (also known as the "phylogenetic signal") in a phylogeny, and phylogenies based upon true genealogical processes give high values of hierarchical structure, whereas subjective phylogenies that have only apparent hierarchical structure (like a phylogeny of cars, for example) give low values (Archie 1989; Faith and Cranston 1991; Farris 1989; Felsenstein 1985; Hillis 1991; Hillis and Huelsenbeck 1992; Huelsenbeck et al. 2001; Klassen et al. 1991). "
29+ Evidences for Macroevolution: Part 1
Cladistic analysis is a test for the hypothesis that species share a common ancestor, just as a DNA fingerprinting method is used to test they hypothesis of guilt.

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 Message 91 by herebedragons, posted 10-24-2016 2:10 PM herebedragons has replied

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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 96 of 279 (793249)
10-24-2016 3:13 PM
Reply to: Message 93 by PaulK
10-24-2016 2:41 PM


Re: Parentless Clades
PaulK writes:
I think that to call common ancestry an assumption is at best an oversimplification. For a start, isn't the use of outgroups a test of that assumption ?
Absolutely, as discussed in the post above.
And on a less formal level, why should cladistics produce a nested hierarchy if it is dealing with disjoint groups ? And surely there are characters - not to mention the genetic evidence - which are naturally explained in terms of common descent.
It is a trivial matter to organize any group of objects or species in to a clade. The test is how many possible trees are there, and how well supported are they.
For example, we could organize automobiles into a clade. However, there are many, many possible trees that are all equal. Do we order them by make? By model? By number of cylinders? By drive train? There are billions of possible trees when organizing automobiles, all equally supported. Not so with life.

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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 98 of 279 (793254)
10-24-2016 4:23 PM
Reply to: Message 97 by Dr Adequate
10-24-2016 4:18 PM


Re: Proposition: Another Angle
Dr Adequate writes:
It's true that we don't have to be closest to one species, but we do have to be closest to something, be it a genus, a family, or whatever. (Aren't chimps in fact a genus, what with the bonobos?)
So you kind of miss my point, which is that the theory of evolution implies that because of the branching nature of evolution, such relationships should be reciprocal. If we are significantly closer to chimps than we are to anything else, then the chimps should be significantly closer to us than to anything else.
Your first paragraph holds the seeds of falsification for your second paragraph. If we consider Pan paniscus and Pan troglodytes as separate species then your second paragraph is false. The closest species to humans is chimps. However, the closest species to chimps is bonobos. It isn't reciprocal.

This message is a reply to:
 Message 97 by Dr Adequate, posted 10-24-2016 4:18 PM Dr Adequate has replied

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