Understanding through Discussion


Welcome! You are not logged in. [ Login ]
EvC Forum active members: 67 (9028 total)
34 online now:
jar, PaulK (2 members, 32 visitors)
Newest Member: JustTheFacts
Post Volume: Total: 884,103 Year: 1,749/14,102 Month: 117/624 Week: 1/95 Day: 1/13 Hour: 0/0


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   Nothing in biology makes sense except in the light of evolution.
Taq
Member
Posts: 8482
Joined: 03-06-2009
Member Rating: 6.1


(1)
Message 4 of 1311 (806562)
04-26-2017 10:52 AM
Reply to: Message 1 by CRR
04-26-2017 4:11 AM


Introns and Exons
Let's look at the first problem.

A eukaryotic gene is made up of introns and exons. When DNA is transcribed into RNA both the exons and introns are made into RNA. However, during mRNA processing the introns are clipped out leaving just the exons which are then translated into protein. The introns are not translated into amino acid sequence.

When we observe homologous genes between species we see that there is more DNA sequence shared between exons than between introns. This divergence between exons and introns roughly increases with the morphological differences between species. However, introns have nothing to do with morphology, so why do we see this trend?

Only evolution is able to explain this trend. Negative selection in the functional exons results in sequence conservation, whereas mutations in the introns are fixed by neutral drift. This produces the divergence between the exons and introns. This divergence increases with evolutionary distance since there has been more time for neutral drift to fix mutations in the introns.

The divergence between exons and introns only makes sense in the light evolution. I have yet to see a single other theory that explains this pattern, or even attempts to explain it in a reasonable, cogent, and testable manner.

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 1 by CRR, posted 04-26-2017 4:11 AM CRR has not yet responded

Replies to this message:
 Message 489 by aristotle, posted 06-16-2017 3:05 AM Taq has responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009
Member Rating: 6.1


Message 8 of 1311 (806695)
04-27-2017 10:36 AM
Reply to: Message 5 by CRR
04-26-2017 11:15 PM


CRR writes:

Let's discuss the article and the extent to which quote "Nothing in Biology Makes Sense except in the Light of Evolution" is applicable today.

That's exactly what I did in message #4 with my example of exon and intron divergence. Perhaps you could start with that example.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 5 by CRR, posted 04-26-2017 11:15 PM CRR has not yet responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009
Member Rating: 6.1


(4)
Message 9 of 1311 (806707)
04-27-2017 10:54 AM


The Nested Hierarchy
One example of a set of observations that dates to before Darwin is the nested hierarchy of shared features. Prior to evolution, there was simply no explanation as to why shared features were distributed in this manner.

Why does everything with fur also have three middle ear bones? Why does everything with a back bone also have a backwards facing retina when some animals without a backbone have forward facing retinas? Why does everything with fur also have mammary glands? Why does everything with feathers have flow through lungs?

There was simply no answers for these questions until Darwin had a Eureka! moment. In fact, you can find that moment immortalized in his very notebooks where he drew this diagram:

The nested hierarchy only makes sense in light of a process with common ancestry and descent with modification, what Darwin called evolution.

I have yet to see a single ID/creationist explain this pattern. There is simply no reason why a designer would force separately created species into a nested hierarchy. When humans design things we don't force those designs into a nested hierarchy. Things like cars, paintings, tools, and buildings don't fall into a nested hierarchy even when they are designed by a single human. There is absolutely no functional reason why life would need to fall into a nested hierarchy. The only explanation we have for this pattern is evolution, and this pattern of shared features only makes sense in the light of evolution.

Edited by Taq, : No reason given.


Replies to this message:
 Message 10 by Chiroptera, posted 04-27-2017 11:15 AM Taq has not yet responded
 Message 16 by RAZD, posted 04-28-2017 9:22 AM Taq has not yet responded
 Message 491 by aristotle, posted 06-16-2017 3:55 AM Taq has not yet responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009
Member Rating: 6.1


(2)
Message 12 of 1311 (806772)
04-27-2017 5:20 PM


Correlation Between Independent Phylogenies
The next example of why biology only makes sense in the light of evolution is the correlation between phylogenies based on morphology and phylogenies based on DNA sequences. In essence, it is a combination of the nested hierarchy and genetic divergence which we have discussed in part in previous posts.

So what is the deal here? Let's use the cytochrome c gene as our specific example. It is a protein that sits in the mitochondrial and pushes protons across that membrane against a concentration gradient. It plays a vital, yet mundane role in metabolism. More importantly, the protein has nothing to do with what an animal looks like (i.e. morphology).

So what happens when we organize animals into phylogenies based on morphology and based on cytochrome c DNA sequences? We get an exact match. The phylogenies are exactly the same. The more physically similar two animal species are, the more similarity there is in their cytochrome c gene, even though morphology and the DNA sequence of cytochrome c are completely independent of one another. You can read more here:

quote:
So, how well do phylogenetic trees from morphological studies match the trees made from independent molecular studies? There are over 10^38 different possible ways to arrange the 30 major taxa represented in Figure 1 into a phylogenetic tree (see Table 1.3.1; Felsenstein 1982; Li 1997, p. 102). In spite of these odds, the relationships given in Figure 1, as determined from morphological characters, are completely congruent with the relationships determined independently from cytochrome c molecular studies (for consensus phylogenies from pre-molecular studies see Carter 1954, Figure 1, p. 13; Dodson 1960, Figures 43, p. 125, and Figure 50, p. 150; Osborn 1918, Figure 42, p. 161; Haeckel 1898, p. 55; Gregory 1951, Fig. opposite title page; for phylogenies from the early cytochrome c studies see McLaughlin and Dayhoff 1973; Dickerson and Timkovich 1975, pp. 438-439). Speaking quantitatively, independent morphological and molecular measurements such as these have determined the standard phylogenetic tree, as shown in Figure 1, to better than 38 decimal places. This phenomenal corroboration of universal common descent is referred to as the "twin nested hierarchy". This term is something of a misnomer, however, since there are in reality multiple nested hierarchies, independently determined from many sources of data.
http://www.talkorigins.org/...1.html#independent_convergence

This only makes sense in the light of evolution. Only evolution would produce matching phylogenies for both morphology and DNA. A designer, especially an all powerful and all knowing one, could create two nearly identical species with genomes that share less than 50% sequence, if the designer wanted to. A good analogy is computer programs. The web browser Google Chrome looks nearly identical on both the Mac and PC, yet the computer code underneath the web browser on the two platforms is very different.

Biology is no different. If you wanted to, you could completely change the anti-codons on the tRNAs. This would allow you to produce identical proteins from very different DNA sequences. This is just one change you could make. Hypothetically, you could produce two nearly identical species from proteins that share very little sequence as well since protein function is very redundant when it comes to sequence.

On top of that, a designer could mix and match genes from very divergent species. For example, a designer could use an exact copy of a jellyfish gene in the mouse genome. In fact, humans have done that very thing, and what resulted was a green fluorescent mouse that is used in scientific research. Even when humans design organisms we routinely violate a matching phylogeny because there is absolutely no functional reason why you would need to have these phylogenies match one another.

In the end, only evolution can explain this overarching and all encompassing observation that exists in biology. The matching phylogenies are a massive part of biology, and only evolution explains it. Those phylogenies make zero sense without evolution.

Edited by Taq, : No reason given.


  
Taq
Member
Posts: 8482
Joined: 03-06-2009
Member Rating: 6.1


(2)
Message 13 of 1311 (806773)
04-27-2017 5:34 PM


Genetic Equidistance
The next example of why biology only makes sense in the light of evolution is the observation of genetic equidistance.

What is genetic equidistance? This is when the % DNA similarity is about the same between two Species A and Species C, and between Species B and Species C.

Let's look at one of those trio of species: humans, mice, and chickens.

Let's also use the same gene from the previous post: cytochrome c.

If we go to Homologene at NCBI, we can search for cytochrome c (cycs) and get a pairwise alignment score for humans, mice, and chickens. What do we get?

Human v. mouse: 90.5% similar
Human v. chicken: 81.6% similar
Mouse v. chicken: 81.9% similar

Human and mouse are genetically equidistant from the chicken. But why? Only evolution can explain this. Again, we go back to phylogenies:

Humans are A, mice are B, and chickens are C. This is the accepted evolutionary relationships between humans, mice, and chickens. As you can see, if you trace A to the node that connects it to C, it is the same node that connects B to C. A and B share the same common ancestor with C, meaning that they evolutionary distance between A and C is the same as the evolutionary distance between B and C. This is why we see genetic equidistance, because humans, mice, and chickens evolved from the same common ancestor, with the human/mouse lineage splitting after it splits with the chicken lineage.

In fact, you can pick any trio you want at Homologene. You can use humans, cows, and frogs. You could do mice, chickens, and frogs. Every time you draw up the evolutionary relationships and make the prediction of where you should see genetic equidistance, sure enough, there it is.

Again, only evolution explains this. This only makes sense in the light of evolution.

Edited by Taq, : No reason given.


  
Taq
Member
Posts: 8482
Joined: 03-06-2009
Member Rating: 6.1


(2)
Message 17 of 1311 (806840)
04-28-2017 11:04 AM
Reply to: Message 14 by Tanypteryx
04-27-2017 7:41 PM


Re: Endogenous Retroviruses
Tanypteryx writes:

Endogenous Retroviruses (ERVs) have left the record of infections in our DNA and the DNA of many other organisms.

ERVs do contain a wealth of information, but once again, they only make sense in the light of evolution.

As you stated, you can find the same ERVs at the same position in the human and chimp genomes. Of the over 200,000 ERVs in the human genome, less than 100 are not found at the same position in the chimp genome. The rest are found at the same position (i.e. orthologous).

One interesting side note is PtERV insertions found in the chimp and gorilla genomes. That same family of ERV is not found in the human or orangutan genome. ID/creationists often argue that the same retrovirus will insert into similar positions in similar genomes. Of course, studies looking at the behavior of retroviruses in the lab completely refute this idea, but we can still do the same thing with PtERV insertions. Since PtERV insertions are not found in the human genome, but are found in the chimp and gorilla genomes, this allows us to predict that these insertions happened after the human and chimp lineages split. Therefore, PtERV insertions should be found at different positions in the chimp and gorilla genome, contrary to the predictions made by ID/creationists.

So what do we see? When scientists mapped the PtERV insertions in the chimp and gorilla genome they found that they were not at the same positions within each genome, completely consistent with the predictions made by the theory of evolution and contrary to the predictions made by ID/creationists. Once again, the pattern and species distribution of ERV insertions only make sense in the light of evolution.

Comparing the ERVs in identical spots in the genomes often show slight differences between species that can be attributed point mutations that have occurred since divergence.

We can also track the changes within the ERV itself in a single species. This is due to a specific characteristic found in ERVs. The retroviral genome is flanked by repetitive DNA called LTRs (long tandem repeats), kind of like bookends on either side of the genome. These sequences serve as strong promoters for the viral genome allowing it to use the host transcriptional systems to transcribe the viral genes. When a retrovirus inserts into the host genome the LTR bookends of the viral genome are identical in sequence. Therefore, we can compare the two LTRs within a single ERV to see how many mutations those sequences have accumulated in a single lineage.

So how does evolution come in and make sense of this? The theory predicts that the longer an ERV has been in a lineage the more mutations it will have accumulated, and therefore the more divergence you will see between the 5' and 3' LTRs (5' and 3' denote the beginning and end of a stretch of DNA). Therefore, an ERV shared by many primate species should have inserted into a common ancestor long ago compared to an ERV found in just humans and chimps, or a single species. The longer an ERV has been in a lineage, the more differences there should be between the 5' and 3' LTRs which allows us to arrange them by their similarities.

When we compare the LTRs between themselves and between species, we get the expected phylogenies.


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC17875/

Once again, this only makes sense in the light of evolution.

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 14 by Tanypteryx, posted 04-27-2017 7:41 PM Tanypteryx has acknowledged this reply

  
Taq
Member
Posts: 8482
Joined: 03-06-2009
Member Rating: 6.1


(2)
Message 22 of 1311 (807182)
05-01-2017 10:49 AM
Reply to: Message 20 by CRR
05-01-2017 6:57 AM


Re: What are you arguing?
CRR writes:

Please state your position. Are you trying to make the case that
a) NOTHING in biology makes sense except in the light of evolution.
b) SOME things in biology only make sense in the light of evolution.
c) for some things in biology evolution provides a plausible but not exclusive explanation.
d) Everything in biology makes sense without invoking evolution.

Dobzhansky was using a bit of hyperbole, but I would say that a massive part of biology does not make sense except in the light of evolution, as detailed in this thread. Evolution is currently the only scientific explanation for these observations, as shown by the absence of any other explanation in the arena of biology or in this thread.

We have given multiple examples now of wide ranging observations that can only be explained by evolution. The power of the theory to explain these observations is driven home by the lack of replies to those posts by ID/creationists. This is why scientists accept the theory of evolution, because it does explain the evidence. It isn't a matter of excluding ID/creationism. There simply is nothing scientific to include from ID/creationism. It doesn't explain the nested hierarchy, the patterns of DNA divergence, the distribution of species across the Earth or in the fossil record, or tons of other observations. Evolution does explain these things.


This message is a reply to:
 Message 20 by CRR, posted 05-01-2017 6:57 AM CRR has not yet responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009
Member Rating: 6.1


(1)
Message 31 of 1311 (807336)
05-02-2017 11:09 AM
Reply to: Message 30 by Percy
05-02-2017 8:42 AM


Percy writes:

. . . but while much in biology requires evolution to make sense, much does not. Biology is a huge field.

A good "counterexample" might be specific observations in physiology. For example, mitochondria store chemical energy by creating a proton gradient across a membrane which involves the metabolism of simple sugars. Evolution doesn't explain why an ATP can be produced when a proton moves from high concentration to low concentration through a membrane bound protein. Thermodynamics does a great job of explaining this process, but evolution not so much.


This message is a reply to:
 Message 30 by Percy, posted 05-02-2017 8:42 AM Percy has acknowledged this reply

  
Taq
Member
Posts: 8482
Joined: 03-06-2009
Member Rating: 6.1


(2)
Message 46 of 1311 (807486)
05-03-2017 10:55 AM
Reply to: Message 32 by Dredge
05-03-2017 12:49 AM


Dredge writes:

Are you saying that without him, biologists would not be aware, for example, that the interplay between mutations and natural selection can produce heritable changes in a population?

Alfred Russel Wallace co-discovered the theory of evolution, so I think it could be said that if Darwin and Wallace had not co-written the first papers on the theory of evolution then someone else would have in short order. One of the interesting side notes of history is that both Darwin and Wallace were constructing the very same theory in complete isolation to one another. This only proves that the evidence had reached a point where the discovery of the theory of evolution was almost a sure thing.

I find it interesting that ID/creationists project their own religious leanings onto science to the point that they think scientific theories are somehow beamed down from some deity. They aren't. If Einstein had not discovered the theory of relativity, then some other scientist would have. If Koch had not discovered germs, then some other scientist would have. If Columbus had not publicized the existence of North America to the rest of Europe, then someone else would have. Scientific theories don't rise and fall because of one person. It just so happens that one scientist is lucky enough to be the first to discover the theory.

Without Darwin, would biologists have discovered drift, lateral gene transfer, recombination, etc, etc?

Since we also had Wallace, the answer would be yes.

If Darwin is responsible for nothing more than coming up with the theory that all life evolved from a common ancestor,

Darwin didn't come up with that theory.

I mean, of what practical use is it to belief that whales evolved from some deer-like creature over a period of 50 million years?

You really are anti-knowledge, aren't you?


This message is a reply to:
 Message 32 by Dredge, posted 05-03-2017 12:49 AM Dredge has responded

Replies to this message:
 Message 58 by Dredge, posted 05-05-2017 5:43 AM Taq has not yet responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009
Member Rating: 6.1


Message 47 of 1311 (807488)
05-03-2017 10:58 AM
Reply to: Message 36 by Dredge
05-03-2017 3:04 AM


Dredge writes:

Yes, sorry; your defintion of evolution is heritable change in a population. So what's this got to do Darwin? Heritable changes in a population has been a known fact for thousands of years.

Darwin was able to show that heritable changes, otherwise known as descent with modification, was responsible for the nested hierarchy that Linnaeus first discovered. He showed how the mechanisms of evolution could produce a wide variety of species from a common ancestor. Before Darwin, species were thought to be immutable and not related.


This message is a reply to:
 Message 36 by Dredge, posted 05-03-2017 3:04 AM Dredge has responded

Replies to this message:
 Message 61 by Dredge, posted 05-05-2017 5:50 AM Taq has responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009
Member Rating: 6.1


(1)
Message 48 of 1311 (807489)
05-03-2017 11:00 AM
Reply to: Message 38 by Dredge
05-03-2017 3:27 AM


Dredge writes:

People were clearly already well aware of the mechanism of natural/artificial selection and its effect on a popularion, so what did Darwin come up with that advanced knowledge of "evolution" (ie, heritable changes on a population)?

This:

Darwin was able to apply observations of biogeography, fossils, and human breeding to the larger field of biology and show how species groups could be linked through common ancestry.


This message is a reply to:
 Message 38 by Dredge, posted 05-03-2017 3:27 AM Dredge has not yet responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009
Member Rating: 6.1


(1)
Message 127 of 1311 (808050)
05-08-2017 10:44 AM
Reply to: Message 61 by Dredge
05-05-2017 5:50 AM


Dredge writes:

Yes, ok, but what difference has believing Darwin's yarn made to anything in the real world?

First, it isn't Darwin's yarn. It is a theory that has been developed over 150 years by hundreds of thousands of scientists.

Second, in the real world we now know the history of life and how species are related. That's the difference.


This message is a reply to:
 Message 61 by Dredge, posted 05-05-2017 5:50 AM Dredge has not yet responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009
Member Rating: 6.1


(1)
Message 129 of 1311 (808054)
05-08-2017 10:48 AM
Reply to: Message 72 by Davidjay
05-05-2017 11:02 AM


Re: Darwin
Davidjay writes:

Yes, totally agree, the theory of evolution contributes nothing to our knowledge of biology, NOTHING,

Then please respond to any of my posts in the first 30 of this thread. In those posts I discuss just how the theory of evolution contributes to our knowledge of biology. For example, it allows us to understand the difference in divergence between exons and introns. It helps us explain the nested hierarchy. It helps us explain the distribution and divergence of orthologous endogenous retroviruses. It helps us explain biogeography. It helps us explain the fossil record. This is just the tip of the iceberg.


This message is a reply to:
 Message 72 by Davidjay, posted 05-05-2017 11:02 AM Davidjay has not yet responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009
Member Rating: 6.1


(1)
Message 130 of 1311 (808078)
05-08-2017 12:03 PM
Reply to: Message 70 by Faith
05-05-2017 10:24 AM


Re: The Definitional word games come from the ToE, not the creationists
Faith writes:

All evolution from the Ark IS microevolution, intraspecies variation built into the genome of the Kind, or descent with modification within the Kind; it's the ToE that forces the idea of macroevolution on us.

How does creationism make sense of the fact that all complex eukaryote species fall into a nested hierarchy?

How does creationism make sense of the fact of exon and intron divergence between different species groups, such as rodents and humans?

How does creationism make sense of pattern of orthologous endogenous retroviruses shared by humans and other primates?

The fact of the matter is that the theory of evolution explains all of these things which makes it useful in the field of biology.


This message is a reply to:
 Message 70 by Faith, posted 05-05-2017 10:24 AM Faith has not yet responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009
Member Rating: 6.1


Message 131 of 1311 (808081)
05-08-2017 12:15 PM
Reply to: Message 87 by CRR
05-06-2017 6:51 AM


Re: 2 - 0. Own goals.
CRR writes:

Moroz? Yes he does disagree; as I noted in my post #53 when I said "What is revealing is that people actively promoting the importance of the theory of evolution admit that it is little used in day to day biology."

That's a bit ironic given Moroz's CV. The very first hit from a Google Scholar search turns up this primary paper:

"Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida"
http://www.nature.com/...nal/v444/n7115/abs/nature05241.html

That's as evolutionary as it gets. Phylogenetic analysis is exactly what the theory of evolution is all about, and Moroz uses it.

Another own goal. Douglas Axe discusses this "evolution" of antennas in Chapter 11 of "Undeniable"* where he says "As a finder of inventions, Darwin's evolutionary mechanism is a complete bust, but as we saw in chapter 7, it sometimes comes in handy as a fiddler. ... Fine tuning involves the adjustment of many small details, so trial and error is often the best way to do it."

In fact I'd say it is more a trial and error solution aided by the power of computers than it is an application of evolutionary theory.

*How Biology Confirms Our Intuition That life Is designed.
Highly recommended.

In which primary paper did Axe show that Darwin's mechanisms were a bust?

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 87 by CRR, posted 05-06-2017 6:51 AM CRR has not yet responded

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2018 by EvC Forum, All Rights Reserved

™ Version 4.0 Beta
Innovative software from Qwixotic © 2021