Sunday, December 16, 2012

Q&A Creationist & Myself: The loss and addition of large DNA sequence blocks are present in humans and gorillas, but not in chimps" even though "the gorilla is lower on the primate tree than the chimp and supposedly more distant to humans. How could these large blocks of DNA--from an evolutionary perspective--appear first in gorillas, disappear in chimps, and then reappear in humans?

Question: The loss and addition of large DNA sequence blocks are present in humans and gorillas, but not in chimps" even though "the gorilla is lower on the primate tree than the chimp and supposedly more distant to humans. How could these large blocks of DNA--from an evolutionary perspective--appear first in gorillas, disappear in chimps, and then reappear in humans?

Response: Though I am unsure of this exact case, and would like to see the article about this…ive heard of something similar. Until I can know exactly what section of DNA they are talking about, I can only give you my best understanding from other examples.  So I believe this is saying that a large section of DNA is present in gorillas as well as Homo sapiens, but is not present in the chimpanzee DNA.  And since chimpanzees are our closer cousins… How can they be in the gorilla and not the chimpanzee?

Example 1- Apes: If section A of chromosome 1 in the last common ancestor of gorillas chimps and humans (around 12 million years ago) contains 1000 base pairs… And when looking at the three species today you only find this section in the gorilla and the human, this simply means that sometime after the chimpanzee broke off from the Homo sapiens lineage around 7 million years ago, they lost this section of the chromosome… And the gorilla and humans have not.  Now again I am unsure what sections of the chromosomes you are speaking of but if these sections are functional DNA then it simply means that the gorilla and Homo sapiens have maintained this section of the chromosome from the last common ancestor, and the chimpanzee lost it. 

Large sections of the chromosomes can be deleted, functional or nonfunctional and if it does not hurt the organism, that deletion will be passed on.  It is not within the deletion that we trace lineages, but within the existence of a specific section of DNA.  Large sections can be lost all the time, but large copying mistakes are beyond rare, and when present in two different species it can tell us that they are related as their common ancestor is the only way that they could both have this exact section.

I did read the article that I believe this was pulled from…(  And the people who wrote this made a critical error when they make the claim that we are not 97% similar to chimpanzees.  This comes from the understanding of genetics…which indeed can be complicated but fascinating.  In short, the authors of this article only compare functional DNA, meaning the part of the DNA that as far as we know codes for actual proteins.  This is the part of the DNA that allows for differences in appearance.  Though this part of the DNA is interesting, it is within the rest of the DNA that our ancestry is found.  This is where the large copying mistakes show up as well as old genes such as genes for tails.  These other genes no longer function, but they are still inherited through the generations.  We can find “fossilized” genes in our genome for all sorts of things…that can only be explained by looking at our ancestry and what their forms looked like.

Example 2 - Blind Cave Fish: A great example of this is within the blind cave fish who though live in caves, and have for millions of years, still possess eyes but are now almost functionless and now develop skin over them.  The only reason it has eyes in the first place is because it inherited eyes from its ancestors who needed them... But now that they have been living in the dark, they have begun to develop mutations in the genes controlling the function and form of their eyes, and now have almost completely lost their ability to see.  We can compare the genes for their eyes to their common ancestor and see that they have inherited the same genes that made functional eyes in a different species but are now breaking apart in the albino fish.  If this fish does not need the ability to see, why have eyes in the first place?  And why did the genes that code for these nonfunctional eyes look so similar to the genes the fish that is considered an ancestor?

Example 3 - Icefish: My last story involves something I actually spoke about on the podcast, and it is one of my favorites. This is about the icefish. I read about them in Sean B. Carroll’s book The Making of the Fittest and this is where ill be pulling most of my information.  .  This fish lives in the South Atlantic Ocean and it completely lacks red blood cells, the pigmented oxygen – carrying cells that until the discovery of these in Arctic ice fish, have been found in every living vertebrate.  Even close relatives of the icefish, such as the in Arctic rock cod and the New Zealand black cod, are red-blooded.  What happened to their hemoglobin?  How can the fish survive without red blood cells?  We have no fossils of this fish so they decided to look into the DNA.  In these amazing fish, the two genes that normally contain the code for the globin, part of the hemoglobin molecule, have gone extinct.  One gene is a molecular fossil, a mere remnant of the globin gene that still resides in the DNA of the icefish, but it is utterly useless and eroding away, just as a fossil weathers upon exposure.  The second globin gene, which usually lies adjacent to the first in the DNA of the red-blooded fish, has eroded away completely. 

This is absolute proof that the ice fish has abandoned the genes for making a molecule that nurtured the lives of their ancestors for over 500 million years.  Over the past 55 million years, the temperature of the southern ocean has dropped, from about 68°F to less than 30° and some locales.  About 33 to 34 million years ago, and the continual movement of the Earth's tectonic plates, Antarctica was severed from southern tip of South America, and became completely surrounded by ocean.  This limited the migration of fish populations such that they either adapted to the change or went extinct, which was the fate of most.  While others vanished one group of fish exploited the changing ecosystem.  The ice fish are a small family of species, within the larger suborder “Notothenioidea, that altogether contain 200 species that now dominate in Arctic fisheries.  The low temperature of the Arctic waters present some great challenges on body physiology.  In Arctic fish, in general, cope with this problem by reducing the number of red cells per volume of circulating blood.  Red-blooded  Arctic fish have about 15 to 18% of their  blood volume made up of red blood cells, when we are at about 45%.  But the icefish have taken this to an extreme, by eliminating red blood cells altogether, allowing their hemoglobin genes to mutate into obsolescence.”

Analysis of the DNA of pale hearted icefish revealed that their myoglobin gene is mutated – an insertion of five additional letters of DNA have disrupted the code for making normal myoglobin proteins.  In these species, the myoglobin gene is also on its way to becoming a fossilized gene.  There are many more genes that have been modified so that all sorts of vital processes can occur in the subfreezing climate.  The adaptation to cold is not limited to the modification of some genes and the loss of others; it also required some innovation. 

Foremost among these inventions is the anti-freeze protein.  The plasma of an Arctic fish is chock-full of these particular proteins which help the fish survive in icy waters.  Without them the fish would freeze solid.  These proteins have a very unusual and simple structure.  They made up of 4 to 55 repeats of just three amino acids, where most proteins contain all 20 different types of amino acids.  Since warm water fish have nothing of this sort, the antifreeze genes were somehow invented by an Arctic fish.  Where in the world antifreeze come from?

It was discovered that the antifreeze genes arose from a part of another, entirely unrelated gene.  The original gene encoded a digestive enzyme.  A little piece of its code broke off and relocated to a new place in the fish genome.  From this simple DNA code, a new stretch of code evolved for making the antifreeze proteins.  The origin of the antifreeze proteins stands out as a prime example of how evolution works more often by tinkering with materials are already available – in this case a little piece of another code – rather than designing new things completely from scratch.  By comparing the states of genes in different icefish, their closest red-blooded relatives, and other in Arctic fish, we can see that certain changes occurring at different stages and icefish evolution.  All 200 or so in Arctic species have antifreeze genes, so that was an early invention.  But only the 15 or so icefish species have fossil hemoglobin genes.  This means that the hemoglobin genes must have been abandoned by the time the icefish species evolved.  Furthermore, while some icefish cannot and do not make myoglobin, some do.  This reveals that the changes in the myoglobin genes are more recent than the origin of the icefish, and disuse of myoglobin is still evolving.  By examining other DNA sequences from each species, it is possible to map these event onto a timeline of geology with the South Atlantic – with the origin of the Antarctic Notothenioidae occurring about 25 million years ago, and the origin of the icefish only about 8 million years ago.

So it is within the addition of these sequences making the anti-freeze proteins that we can find the ancestry for the icefish as this digestive enzyme duplication can only arise in this specific way once. And the genes that the icefish no longer need, like genes for hemoglobin and myoglobin, are now eroding away, showing they used to have functional ones but now are just inheriting broken genes, representing their heritage.

Sean B Carroll’s Book -

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