Why is it that genetic similarity = common descent? Isn't that an interpretation not an observation?


#1

I would be interested the opinions of the brainiacs and learned folks at BioLogos on in this layman’s opinion of how “common descent” is interpreted by evolutionary scientists with respect to its relevance to applied biology:

From the outside looking in, it seems to me that when evolutionary scientists see genetic similarities between organisms, they automatically interpret this as “common descent” - they do this because they consider that there is simply no other atlernative to explaining such genetic similarities but common descent. Therefore, in there minds, Genetic Similarities = Common Descent, by default.

For example, I’ve come across evolutionist literature that claims the theory of common descent has proven useful in developing swine flu vaccine. But I suspect that that what they mean is, it is genetic similarities between the organisms involved that has proved useful. The usefulness of these similarities exists regardless of whether one accepts the theory of common descent or not.

As a creationist, I could claim that such genetic similarities exist because all organisms were created by the same Maker, who decided to use the same molecular “building blocks” for all life forms. But I wouldn’t claim that Creation has thus proven useful in developing swine flu vaccine, because this is an interpretation of the facts that is neither useful nor relevant to science.


Does biology need the theory that all life shares a common ancestor?
What do people think of "progressive creation"?
(George Brooks) #2

@Dredge

Have you ever had a project in school, where you had to figure out what was related and what wasn’t? Languages? Categories of literature? The blossoming of certain kinds of sports?

How would you tackle such a project? All these things that we study (from Ants to Zoophytes) are all embedded in a timeline, right? So one looks for indications of relatedness that seem to be more than just coincidence, right? And you are looking for a sequence of similarities and differences which make chronological sense!

If a Fish and a Bird share the exact same kind of cellular chemistry about a specific chemical, an Evolutionist would expect that this is a very common chemistry that would be in fact shared by much more than Fish and Birds. Why? Because there’s no evolutionary model that would predict that the body chemistry, in common between Fish and Birds, would not be shared even more widely.

But if we have a chemistry shared between Fish and Amphibians, but not with lizards, one might expect that Fish and Amphibians are more closely related than Fish and Lizards. But, at the same time, if you look at a different genetic trait, and you see similarities between amphibians and lizards, you start to think: ah, maybe the amphibians are “the middle men” between fish and lizards. And so on. This is common sense stuff, @Dredge.

You seem to think that genes acknowledge some limit to their ability to allow or enforce changes on a living thing. How would that happen? The only thing that actually does tend to slow down population wide changes is a large population of stable variants. If a mutation happens here or there in a large population, it is more likely to be drowned out by the sheer “noise” of the pre-existing genetic variability.

So speciation becomes less likely with population size. Not too surprisingly then, when a population is being decimated by a new environmental situation (either a new rival for the same food, or the extinction of a once plentiful food source), the population size begins to contract. And the smaller the population becomes, the more significant each new mutation or variant combination becomes. In a now tiny population (sometimes called a “bottleneck”), a beneficial change can explode within the ranks of the population, and come to easily predominate as the old guard genes become less and less able to perpetuate within the population.

You get this, right? So, try to imagine then, what happens if you have one large population, unified, even as members of the population range across various geographies and climates. If there is robust exchange of genetic factors throughout the range … from East to West, from North to South, and so forth, then new variants are going to have a difficult time prevailing when the “noise” of the existing variants drown them out.

But if the free flow of exchanging genetic factors becomes interrupted … by distance or by barriers … then what was once one very large population has now become 2 or 3 smaller groups. Perhaps 1 group is half the originally unified population, and a second group is one third the original population, that means the third group is a tiny fraction, about 12% of what used to be a unified population!

Over time, this 12% could do one of the following things:

  1. become extinct.
  2. eventually move back into closer contact with its original population source. Or,
  3. continue to change in a direction that eventually reduces reproductive compatibility with the other populations, and thus close off further external exchange of genes to virtually nothing!

When (3) happens, it means that population can start to change much more quickly than those other groups that continue to have a robust exchange of genetics!

So how would you figure out which group was the original group? Wouldn’t you look to see which odd-ball genetic factors exist in more than one group, and which factors belong to all of them? Wouldn’t you make a common sense investigation of genetic factors that indicate a straight line of change, rather than changing from “A” to “B” … and then proposing that a specific group ended up returning to “A”? One would not expect this very often, right?

In an Eskimo village where one very famous hunter had red hair, and appears to have produced a great number of children and great grand children with red hair. If you came back to the village after 50 years and you found that the one village was now four villages. Would you expect the village with mostly red-headed people in it to be unrelated to the famous hunter, but that it was the black-haired villagers who were most closely related to the red-headed hunter? Why would anyone propose a scenario like that? It could happen, I suppose, but one would find indicators for how that happened. One wouldn’t expect it to happen all the time as a general rule, right?

Here is a narrative treatment that someone must have written just for you!:

Evidence from Biochemistry
"Evidence for common descent may be found in traits shared between all living organisms. In Darwin’s day, the evidence of shared traits was based solely on visible observation of morphologic similarities, such as the fact that all birds—even those which do not fly—have wings."

"Today, the theory of common descent is supported by genetic similarities. For example, every living cell makes use of nucleic acids as its genetic material, and uses the same twenty amino acids as the building blocks for proteins. All organisms use the same genetic code (with some extremely rare and minor deviations) to specify the nucleic acid sequences that form proteins. The universality of these traits strongly suggests common ancestry, because the selection of these traits seems somewhat arbitrary."

“Similarly, the metabolism of very different organisms is based on the same biochemistry. For example, the protein cytochrome c, which is needed for aerobic respiration, is universally shared in aerobic organisms, suggesting a common ancestor that used this protein.”

"There are also variations in the amino acid sequence of cytochrome c, with the more similar molecules found in organisms that appear more related (monkeys and cattle) than between those that seem less related (monkeys and fish)."

“The cytochrome c of chimpanzees is the same as that of humans, but very different from that of bread mold. Similar results have been found with blood proteins.”

“Other uniformity is seen in the universality of mitosis in all cellular organisms, the similarity of meiosis in all sexually reproducing organisms, the use of ATP by all organisms for energy transfer, and the fact that almost all plants use the same chlorophyll molecule for photosynthesis.”

The closer that organisms appear to be related, the more similar are their respective genetic sequences. That is, comparison of the genetic sequence of organisms reveals that phylogenetically close organisms have a higher degree of sequence similarity than organisms that are phylogenetically distant."

“Comparison of the DNA sequences allows organisms to be grouped by sequence similarity, and the resulting phylogenetic trees are typically congruent with traditional taxonomy, and are often used to strengthen or correct taxonomic classifications.”

“Sequence comparison is considered a measure robust enough to be used to correct erroneous assumptions in the phylogenetic tree in instances where other evidence is scarce.” "“For example, neutral human DNA sequences are approximately 1.2 percent divergent (based on substitutions) from those of their nearest genetic relative, the chimpanzee, 1.6 percent from gorillas, and 6.6 percent from baboons (Chen and Li 2001; Cooper et al. 2003).”

"Further evidence for common descent comes from genetic detritus such as pseudogenes, regions of DNA that are orthologous to a gene in a related organism, but are no longer active and appear to be undergoing a steady process of degeneration. Such genes are called “fossil” genes. Since metabolic processes do not leave fossils, research into the evolution of the basic cellular processes is done largely by comparing the biochemistry and genetics of existing organisms."

"The proteomic evidence also supports the universal ancestry of life. Vital proteins, such as the ribosome, DNA polymerase, and RNA polymerase, are found in everything from the most primitive bacteria to the most complex mammals. The core part of the protein is conserved across all lineages of life, serving similar functions."

“Higher organisms have evolved additional protein subunits, largely affecting the regulation and protein-protein interaction of the core. Other overarching similarities between all lineages of extant organisms, such as DNA, RNA, amino acids, and the lipid bilayer, give support to the theory of common descent.”

“The chirality of DNA, RNA, and amino acids is conserved across all known life. As there is no functional advantage to right- or left-handed molecular chirality, the simplest hypothesis is that the choice was made randomly by early organisms and passed on to all extant life through common descent.”

[End of Narrative Section]

http://www.newworldencyclopedia.org/entry/Evidence_of_evolution


(Richard Wright) #3

Hi Dredge,

What I think would be useful for you to do is read some of the many articles in the Evidence for Evolution section of this site, which cover evidence for common descent from genetics and from other spheres of science. As a heads up, the evidence for evolution is a lot more than comparing DNA strands then claiming, “Ah ha! Common descent!”. I think it’s best when one starts looking into the evidence that supports evolution to go right back to Darwin, what he discovered on his trips, and how he came up with the reasoning behind the concept of common descent.


(Robert J. Kurland, Ph.D.) #4

That is a fine exposition. Thank you!!


(Lynn Munter) #5

The difference is in how these similarities are organized. Is the degree of similarity or difference between any two given organisms predictable from your creationist point of view?

Let’s suppose we want to take Genesis in the most literal possible sense as describing categories of living things. (I don’t know anybody who actually espouses what I’m about to describe, but I think it’s a useful thought experiment to examine.) We have the category of vegetation, with two sub-categories, plants with seeds and trees with fruit with seeds. (The King James and some other translations offer three categories: grass, herbs with seeds, and fruit trees.)

It is a bit tricky to determine how many categories of creatures in the water there are: great sea creatures and teeming or swarming living things. But it seems clear there is only one category of birds (flying things).

It is more clear that land animals have three subcategories, though they vary a bit in how they are translated: livestock (or cattle), creeping (or crawling) things, and wild animals (beasts of the earth). And then humans, male and female.

The Bible then repeats the main categories of living things: fish, birds, all living things that move on the ground; plants with seeds, and trees with seeded fruit.

I have not copied down the repeated refrain of “according to kind” or “all sorts of” that indicates many subtypes within each larger category, but it appears after each subcategory except humans.

So at face value then, we have an outline of how God created, and it is pretty simple to compare this shape to an evolutionary tree of life, which has mammals, birds, reptiles, amphibians, bony fish, cartilaginous fish, various other branches of vertebrates and invertebrates, including insects and shellfish, and all these branches eventually leading back to a common trunk with fungi and plants and microorganisms.

Knowing that the genetics of any individual is largely but not entirely the same as the genetics of its parents, how might it be possible to trace lines of descent by looking at lots of individuals’ DNA? If you had any genetic data you wanted at your fingertips, do you think you could objectively tell which model best fit the data?

Spoiler alert: the super-literal Genesis version is totally inadequate next to a model of common descent. This is why no one tries to use it this way. But the point of the thought experiment isn’t that you should use the model I described above, but that even an attempt to dodge the issue by providing an extremely vague model (“genetic similarities exist because all organisms were created by the same Maker”) doesn’t work, because we can still compare what we see in a bunch of genomes to your model and to the common descent model, and common descent still has a far better match to the data. Genetic similarities and differences are grouped along different ‘branches’ of descent in a way that they would not be if Someone spent a week inventing every kind of creature He could think of.


(Phil) #6

Greetings, and while I will not claim brainiac status and my learning is still a work a progress, I would make a comment about this statement.
It indeed sounds reasonable, and to a certain extent I agree as there may well be just one way things work well and the common building block idea is reasonable.
Where it becomes problematic is when you look at some of the characteristics of the building blocks, and you see flaws in their substance that they have in common. With DNA, these flaws may be mutations, and sometimes those flaws can be found to be due to old viral insertions etc. Just like you can conclude from looking at blocks and determine which were cast by a mold with a flaw then used in building a structure, concluding that the structures were related in space and time, so can you conclude that flaws in DNA that are shared come from a common source. There is no reason God would have put the same order of flaws in the DNA of species, but it relates closely with what we previously suspected, with a few surprises here and there that are delightful to find.


(Curtis Henderson) #7

Common descent is often the most straightforward and reasonable explanation for observation of genetic similarities. Dr. Dennis Venema, BioLogos’s “Fellow of Biology” likes to explain DNA variation over time using the analogy of a true language (more info here).

Dr. Venema likes to use English as an example, but let’s take a look at a different example - Spanish and Portuguese. Without knowing any of the European geography related to the languages, one can easily see the similarities and arrive at the conclusion that they are closely-related and probably diverged fairly recently. Further, it is also intuitive to see similarities to other Romance languages and conclude a common origin, with a more distant “divergence point” in the past. The same types of conclusions can be made for observed DNA similarities. Common descent just plain makes sense.


(Benjamin Kirk) #8

[quote=“Dredge, post:1, topic:36023”]
From the outside looking in, it seems to me that when evolutionary scientists see genetic similarities between organisms, they automatically interpret this as “common descent” - they do this because they consider that there is simply no other atlernative to explaining such genetic similarities but common descent. Therefore, in there minds, Genetic Similarities = Common Descent, by default.[/quote]
Utterly false. What you’re trying to pretend are mere “similarities” are in reality congruent nested hierarchies.

What shows common descent is not mere similarity, but the nested hierarchies mathematically derived from protein and DNA sequences. In addition to the nested hierarchy we see when analyzing sequences of orthologous proteins in different organisms, we also see nested hierarchies for protein families within and across organisms.

I don’t. What proved useful was nested hierarchies.

You could, but that doesn’t begin to explain the way in which the nested hierarchies converge and are superimposable–both for the organisms and their components.

Designed objects can be put in multiple nested hierarchies. Common descent predicts only one. See the difference? See why you pretend that nested hierarchies are mere “similarities”?

Do you see that you are not disputing mere interpretation, but literally misrepresenting the actual evidence?


(Jon) #9

What is your explanation for nested hierarchies?


#10

[quote=“Jonathan_Burke, post:9, topic:36023, full:true”]
What is your explanation for nested hierarchies?
[/quote]I can’t expalin why The Lord created things the way he did. Maybe he started with a basic design and then expanded on it, resulting in a nested hierarchy. But I’m just guessing.
Nested hierarchies fit the evolution model well, I must admit, but the existence of nested hierarchies doesn’t prove that the a literal, six-days-of-creation interpretation is false.


#11

I was going to invite you to my birthday party, Lynn, but now I’m having second thoughts.


#12

Thank you for your extensive post (#2), George. It contains some very interesting facts, esp the biochemistry and genetics stuff.

Isn’t it amazing how the Creator has used similar biochemical mechanisms in vastly different organisms? For example, your post mentions how Cytochrome c performs a similar function in mold to what it does in humans? Fascinating!


(Phil) #13

Harking back to the common "flaws " in the building blocks idea, here is a good article discussing viral insertions and how they show relatedness. Again, the shared pattern if insertions argue against the common building block idea mimicking evolution, as why would the building blocks have the same flaws?


#14

[quote=“jpm, post:6, topic:36023, full:true”]Just like you can conclude from looking at blocks and determine which were cast by a mold with a flaw then used in building a structure, concluding that the structures were related in space and time, so can you conclude that flaws in DNA that are shared come from a common source. There is no reason God would have put the same order of flaws in the DNA of species, but it relates closely with what we previously suspected, with a few surprises here and there that are delightful to find.
[/quote]
I take your point. On the face of it, I don’t know how a creation model could explain such flaws.

Can said flaws be linked to a particular function or physical feature?

P.S. I’ve just seen your latest post (#13). I’ll check out that link. Thanks.


#15

I can relate to this - a little hobby of mine is studying two Romance languages, Italian and French.


#16

Thanks. I’ll look them up.


(Benjamin Kirk) #17

You’re making progress, but you’re still fudging the evidence itself.

It’s not merely nested hierarchies, but nested hierarchies for both the organisms and their components.

It’s not merely fitting the model, it’s making correct predictions.

And science isn’t about proof, it’s about predicting new evidence. Does a creation of separate kinds predict convergent nested hierarchies? Do any designed objects fit in a single nested hierarchy that is superimposable on the nested hierarchy that comes from a mathematical analysis of their components?

The key words here are single and superimposable, Dredge.


(Jon) #18

Well that’s the problem, the more science we do the more we find that life looks like it evolved. Why would God create life deliberately to look like it evolved, if it didn’t? And why is it that it’s scientists who are telling us all about life, and making accurate predictions? We don’t find people figuring this stuff out from the Bible.


#19

That is false. If scientists were to find a living or fossil species that had a mixture of mammal and bird features, then that would actually falsify common descent. Scientists are NOT saying that simply having similarities is what evidences common ancestry. It is a statistically significant phylogenetic signal in both the morphological and genetic data that evidences evolution. It is the nested hierarchy that evidences evolution, not simply having similarities.[quote=“Dredge, post:1, topic:36023”]
As a creationist, I could claim that such genetic similarities exist because all organisms were created by the same Maker, who decided to use the same molecular “building blocks” for all life forms.
[/quote]

We see more than simply sharing the same building blocks. You can have a non-nested hierarchy while still using the same building blocks. For example, a creator could use the same building blocks to create a species with feathers and mammary glands that also has gills. This would be a serious violation of a nested hierarchy, but such a creature could be created by a common creator.

There is simply no reason why we would expect to see a nested hierarchy if ID/creationism is true. The only reason we would expect to see a nested hierarchy is if evolution is true.

http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_03


#20

Then what would show a literal, six-days-of-creation interpretation to be false?