Vestigial genes. Putting Darwin to the test again.

Hi All,


A very interesting piece of research published online. It’s about testing Darwin, this time by predicting the occurrence of vestigial genes then going looking for them. It’s also about an interesting interplay between fossil, and molecular data.

The following is my brief and layman’s attempt to explain it. I offer a link at the end to an explanation given by other scientists.




Darwin devoted a significant portion of his main work The Origin to vestigial or rudimentary organs. He claimed that such organs arose naturally out of his theory. They are to be expected as an outcome of evolution.

One hundred and fifty years later, and with the discovery of the system which controls orgasmic development and hence the development of organs, the question could be asked, if vestigial organs occur, then what about vestigial genes?

Well, at this online link:-

PLoS Genetics: Molecular Decay of the Tooth Gene Enamelin (ENAM) Mirrors the Loss of Enamel in the Fossil Record of Placental Mammals

researchers put Darwin to the test, with respect to a system they reckon should show him to be correct.

Most placental mammals have teeth which are covered with a very hard substance called enamel. However, some mammals have no teeth at all while others have teeth but with no associated enamel. Those with enamel? Well of course there is us and our cousins, the other apes. Cows, sheep, pigs - all have it too. Those without teeth are pangolins, baleen whales, and anteaters. They eat soft stuff. Those with teeth which have no enamel are sloths, armadillos, aardvarks and pigmy and dwarf sperm whales. These too are into the soft stuff.

Scientists have a good understanding as to how enamel forms in the growing embryo and enamel itself, because of its hardness, fossilizes very well in comparison to bone. What is more, evidence shows that mammals descended from animals that themselves had enameled teeth.

Now we all know what vestigial organs are. They are useless or nearly useless organs, or organs which have departed in function from their original one (that is they are vestigial with respect to that original function.) If organs can be vestigial then so can genes. After all, genes give rise to organs. In this particular case, scientists reasoned that if some mammals have no teeth or teeth without enamel and all mammals descended from toothed critters, then they should be able to find vestigial genes in these mammals.

And what would a vestigial gene look like? It would be a gene corrupted by frameshift mutations and/or stop codons. The latter are fairly obvious. They tell the gene decoding mechanism to stop decoding, and one of these in the middle of a gene would render the gene useless. A frameshift mutation is the insertion or deletion of one or a few bases into or from a gene. Remembering that sets of three bases code for an amino acid which then join with other amino acids to make protein, then an insertion of a new base or two is certainly going to mess up the coding down stream from the insertion.

So the scientists picked on an enamel gene called ENAM went looking for it in a database of genes which included 47 species of placental animals representing those with teeth, and those with teeth but no enamel and those with no teeth. These latter two groups constituted 20 taxa in all.

They found the genes and looked for frameshift mutations and stop codons inside them.

From these genes they drew a phylogenetic tree or a family tree if you like. They ensured the veracity of their tree with those derived from other methods (different molecules and genes, or morphologies). Then on that tree they overlayed the results of their search for frameshift mutations and stop codons.

And what did they find? Sure enough, for those mammals with enameled teeth, the genes were clean. However, for 17 out of the 20 taxa having teeth with no enamel or no teeth at all, frame shift mutations and/or stop codons were found.

As predicted, the genes were there, and they were corrupted. They were recognizably the same genes but they had one or more stop codons or frameshift mutations within the genes themselves.


However, that’s not all. Scientists can make estimates of the kind of evolution that was taking place. The methodology can in practice be a bit controversial and tricky, but the idea is fairly simple. There is redundancy in the genetic code. In many cases, several different sets of thee base pairs code for the same amino acid. Thus, changes to a base pair need not lead to a change in an amino acid and hence a protein’s function. In other cases, a change will lead to a new amino acid and therefore a change in the protein’s function. (This is not hard and fast however. For example, some amino acids are similar to others and so if a change is between these acids, then there may be little change to protein function. Or parts of proteins contribute little or nothing to a protein’s function and so changes in these regions may have negligible effect.) Changes to bases which lead to different amino acids in the final protein are called “non synonymous substitutions”. Changes to bases which retain the same amino acid are called “synonymous substitutions”. So by comparing a mutated gene with say a wild type gene, researchers can get an idea of the ratio of non synonymous to synonymous substitutions. If selection is, or has been acting, then there should be a skew in this ratio. If evolution has been neutral, then the rates should be the same. This is because non synonymous substitution, by changing the protein, may be selected for (+ selection) or may be selected against (- selection), whereas synonymous substitution offers nothing for selection given that the protein does not change.

In the research, the scientists did these calculations.

They found that those branches on the tree leading to animals with enamel evolved under what is called “purifying selection”. This kind of selection acts against genetic diversity. Changes to amino acids are selected against. And this is understandable. If you are an organism on a tough diet, as most mammals are, then fiddling with the enamel may be fraught with danger. However, they found that the branches for the animals with no enamel (or no teeth) had ratios showing neutral or near neutral evolution. Again, this made sense. An organism that may have had enamel, would, on moving to an easier diet, have no need to retain enamel, and at this point, any mutation knocking out the enamel gene would not be selected against. The animal could obtain its food, with or without enamel and with or without teeth. Mutations would “pile up” at the same rate in both kinds of DNA codons, those leading to new amino acids and those which don’t. There would be no selective pressure to remove a bad mutation or to retain a good mutation. (I quoted the words “pile up” because its not as if these genes end up with thousands of destructive mutations. There are only a few, but they are easily spotted. Mutation rates have numbers like 0.0003 changes per site per million years. However, given thousands of sites in a gene, these harmful mutations, while few in number, do show up).


And there was more to come. By looking at the combined fossil, gene, and substitution ratio data, the researchers attempted to construct a history of enamel or tooth loss in those branches that had undergone these changes. Most of their article is concerned with reconstructing these histories. In the process, this reconstruction provides clues to palaeontologists as to what kinds of fossils they may expect to find in the future.

The article has several good pictures showing their reconstructed histories. It is well worth a look.


Anyway, this is a longish essay and will probably not be read by any creationists or IDers. A pity. Just another example of how ToE backs its claims with experiment and observation.


There is a very good description of this research at:-

Dead genes for tooth enamel Why Evolution Is True



Regards, Roland

Very interesting read. I've known about vestigial genes for years but this is a much better example than the one I typically use.

Thank you for posting.

__________________

I always like the fish gonads, human gonadal migration leading to a week spot in the abdominal cavity, ultimately leading to male hernias. OUCH!

__________________
We are surrounded by endless forms, most beautiful and most wonderful, and it is no accident, but the direct consequence of evolution by non-random natural selection - the only game in town, the greatest show on Earth. ~R.D.

Originally Posted by rjw

Hi All,
Darwin
devoted a significant portion of his main work The Origin to vestigial organs.
He claimed, such organs arose naturally out of his theory.

Hi Roland,
Claims,
by all sorts of people, holding fast to nameless theories,
observing that & this, for favored estimations,
reasoning something else too, & reckon, it should work;
but
how often does it, do just what was claimed?

Originally Posted by rjw

Scientists have a good understanding...

They do??? - Well, in that case: No more Arthritis. Brain-injuries are no worries. and
Cancer is totally healed, all of them, before they even began, right?

No??? - hmmm, maybe they don't, understand as they
assumed.
Oh well, back to the Drawing-board - There's enuf crayons, for each scientist

Originally Posted by rjw

as to how enamel forms in the growing embryo and enamel itself,
because of its hardness, fossilizes very well in comparison to bone. What is more,
evidence shows that mammals, descended from animals that themselves had enameled teeth.

Really. - See, God is pretty smart! because
He Created animals with enameled-teeth,
who begat off-spring... with enameled teeth.
God is the most Intelligent force, as the evidence continues showing!

Originally Posted by rjw

However, that’s not all. Scientists can make estimates,
of the kind of evolution that was taking place.

Estimates, eh?: as in gauge, calculate, approximate,
voice an opinion, ie judgments, based on guesswork.
hmmm,
but for all their estimating, the Evidence continues
lacking..., particularly about that evilution THEORY:
Brilliant scientists, long ago saw it for what it was,
so hopefully others will also figger it out.

Originally Posted by rjw

After all, genes give rise to organs.

what a profound Observation!, by those scientists.

Do all evolution-scientists also Agree? that
*pluripotent, undifferentiated Stem-cells* including therefore in adults,
as they re-grow their body, are the same as in infants;
albeit adults accumulated more mistakes along the way.
-
Cause with that Regenerative-awareness, (sans organ-donation),
most organs could by their own owners be regrown...

Originally Posted by rjw

In this particular case, scientists reasoned
that if some mammals have no teeth, or teeth without enamel
and all mammals descended from toothed critters, then
they should... be able to find.....

no MERCURY-fillings?; or crowns?????? no, no, no!
what they found were >DENTURES<
roflol
(oh dear, I just laughed so hard-LOL-LOL-
I blew cold tea up my nose!!)

Originally Posted by rjw

And there was more to come. The researchers
attempted...
Researchers put Darwin to the test, with respect to a system
they reckon, should show him to be correct:Why Evolution Is True.
The methodology, can in practice be a bit controversial and tricky, but the idea is fairly simple.

How's this for a "fairly simple idea": Atheists should reckon,
that what GOD invited them to do in the 1st. place,
(nicely summarized by one in CF):
1. Admit they were wrong, and have need to Change...
&
2. Accept God/Jesus Christ as her/his personal Savior.
&
3. Study Science, for the magnificent Learning-adventures,
God created us humans for... - was/IS Right, all along.

Simply KEWL!!!!

Originally Posted by rjw

Anyway, this is a longish essay and
will probably not be read by any creationists or IDers. A pity.

Regards, Roland

re "probably": and you would know that how?

Golly, have you any idea, the amount of Valuable... research,
is being conducted as we speak: for (harmlessly, as in First, do no-harm)
helpfully helping people HEAL...by awakening inside of people,
their own internal Healing-resources, by Empowering these,
so people can again Enrich their own life.
Sure,
it's not as $lucrative$, as what passes for science so often,
but few are the works finer, than playing whatever part,
in people excitedly-jumping up & down, with: "I'm dis-ease FREE"

Now, that's not just a theory; it's Experienced-evidence...science.

Good day!

__________________

This is an example of the nature doing just what the ToE claims.

What? Evolution is well understood, as a result it is helping us to make great progress in these fields of medical research, but just because we know how it happens doesn't mean we instantly have the cure.

You are quite obviously the one who does not understand.

That's nice of you... willing to share. But I'm sure the scientists will manage just fine with their own writing implements.


Yes, because eating and breathing through the same tube is a great idea, as is only being able to see an extremely limited spectrum of light, and having a *ahem* "recreation ground" right next to waste disposal.

No, as in informed, educated judgments that are later confirmed by evidence.

How many times do we have to tell you IDiots that the vernacular "theory" (an idea that you just came up with right then) is in no way the same to the scientific theory, which is supported by all evidence and refuted by none.


And what a profound inattentiveness that you didn't even realize this was the OP's attempt to simplify it into laymen terms so that people like you who are too lazy to read the scientific report could understand it.

So scientists are in the process of better classifying how stem cells work. Stem cell research is not equivalent to the theory of evolution. What point are you trying to get across?

So, you wouldn't mind if I just came over and took your kidney? I promise you wouldn't even notice, I'll use sedatives. After all, you could just regrow it later, couldn't you? Someone could make a lot of money on the black market organ farming from these "aware" people.


What are you talking about?

And of course now you push the faith issue. Because evolution is obviously part of the atheist agenda. Because no true christian could ever believe in evolution. Because you are willfully ignorant about science, so therefore it must be wrong.


Because the vast majority of people who would dismiss this as false (ie. people like you) generally don't have the attention span to make it through an entire scientific paper. Judging by the fact that you did not reference the paper at all, I'd say you fall nicely into his probably.

Golly, no I didn't! Mostly because that's comlete bull. You can improve your natural immune system, but you can't will disease away. You can mentally block the pain, but you can't regrow an arm. I would be very interested if you would provide some evidence, but right now you just look crazy.

Personal testemony is never sufficient evidence. An outside observer, seeing and recording results is. Science does not rely on experienced "evidence" it relies on empirical evidence, ie. the stuff that's actually there.

Good day!
And for the love of all that is good, read a science book, you're embarising.

__________________
"We can easily forgive a child that is afraid of the dark, the real tragedy is when people are afraid of the light"
-Plato

You found a way to pick through a page of information without ever addressing the main idea. That requires talent.

__________________

Thank you Biologist.

I work hard to understand these articles, but enjoy reaching a point of some understanding and being able to tell other folk about it.

The beauty about PLoS is that it is on-line. Nature and Science though are not - and they often have reports on some very interesting research.



Regards, Roland

Gidday sk8Joyful,

The name of the theory is well known. It’s called “the theory of evolution” (ToE). It’s also known as “descent with modification”.

I am not sure what you are arguing here. The scientists were using genetic data and fossil data to confirm an aspect of Darwin’s theory. Confirming theories is a major part of science.

But I did not claim any of this, did I. What I wrote was the following:-

“Scientists have a good understanding as to how enamel forms in the growing embryo and enamel itself, …”.
I never made any claim about arthritis, brain injuries or cancer, did I? If you think I did, then please show me where.

Let me ask you s8Joy – if you had written “I know why Sally went to town”, what would you think of me if I then replied “So you claim to know why Sally went to town, why Jack stole that money, and why Anne got married”?

You make no mention of Jack and Anne in your Sally comment. So why pretend that I made mention of cancer and arthritis in my comment?

The aim of science is to solve problems by using laws, principles and ideas we know and understand. Hence we can now, via this research, gain an idea as to why most mammals have enamel but some don’t. Those that don’t had their enamel genes messed up because they no longer needed the hard enamel, given their diets. Until now, we could only guess that they had messed up genes. Now we know.

And we know how genes do get messed up. It’s standard genetics. We know how messed up genes get passed on. It’s conventional hereditary.

If you wish to posit God as the alternative scientific explanation then:-

1) What empirical evidence do you have to show that God created the three different kinds of animal – those with enameled teeth, those with teeth but no enamel, and those with no teeth?

2) How did God make these enameled teeth? Can you give me an explanation with evidence to support said explanation?

3) How did God make the teeth without enamel? Can you give me an explanation with evidence to support said explanation?

4) Why did God make the jaws with no teeth?

A lot of science is estimation. And because its an estimate, it does not mean that it is a guess. Are you trying to tell me that every time you estimate something, it is little better than a guess?

At this point I must ask s8Joy – did you read my essay for comprehension, or did you merely skimp it for key words to comment on?

The essay and most particularly the research article the essay was based on were about evidence. The scientists supplied it and wrote about it. You can even go online and get the data they used. The links are presented at the back of the online article.
That comment was made as a part of a chain of logical reasoning. (Actually, just as I can quote you YECs who deny that the earth orbits the sun, rather they say that the sun orbits the earth, so I can quote you a YEC who denies that there are genes for limbs and knees.)

???

???

I don’t know how many of the researchers were atheists? Take the US as an example. Given that more theists there accept evolution than do atheists, then possibly some or all of those researchers were theist and possibly Christian at that. Before you lose another cup of tea up your nose, think carefully about what I said above, and do your sums.

(Unless of course you are one who argues that if a person accepts evolution, then they must be an atheist. If so, I know several conservative Christians who would be amused to learn that they are atheists.)

From some 13 years of arguing, debating and discussing with YECs and IDers, including a 2 year exchange of letters with three members of AiG in Australia back around 1996. Two of those men (Dr Safarti and Dr Walker) had PhDs and the third (Mr Lamb) had a BSc.

Do you have any idea of what I do know and what I do not know?

?

All of science is theory.

Evidence is only a part of science. It’s the thing scientist collect so that they can test their theories, be they the atomic theory of matter, theories of gravity, germ theory, heliocentric theory, …

See you later.



Regards, Roland