The Common Ancestry Thread

by cantleave 271 Replies latest members adult

• 

  PSacramento

  I don't know if we can say that transpoons, for example, never had a purpose.

  We can say that, as mammals, they never had a functional prupose, but what about before that?

  Here:

  Transposons, and ENCODE

  We previously examined transposons in our series on “Junk DNA.” In brief, these are parasitic DNA sequences that serve to replicate themselves and spread within genomes. They have sequences that act to recruit host enzymes for making mRNA and a protein enzyme that acts to copy and/or move the transposon to a new chromosome location. These entities are veritable beehives of biochemical activity, but biologists consider them non-functional (with respect to their hosts) even if they are highly functional (with respect to the transposon). In many cases, however, transposon sequences in mammals are defective—they have picked up mutations such that they no longer make the enzyme they need for movement, or perhaps the mutation ruined one of the DNA sites the enzyme binds to. As before, these sequences are non-functional with respect to their mammalian host—they make no contribution to the host organism at all—and they are non-functional even to themselves (since the transposon cannot replicate any longer). Even such doubly non-functional sequences, however, will retain detectable biochemical activity. Host DNA-binding proteins will still bind to these sequences, mRNA may be produced, and even the transposon enzyme might be partially made as a non-functional protein. These biochemical activities may persist for thousands of generations before additional mutations silence them, so these sequences would still be identified as “functional” according the ENCODE criteria. Since almost half of the human genome is made up from such repetitive sequences, it’s not surprising that ENCODE found so much “function.” Yes, these sequences have detectable biochemical activity, but that’s not surprising at all, given what we know about transposons. Nor does such activity demonstrate that these sequences are functional in the more strict sense. Indeed, lines of evidence from comparative genomics strongly suggest they are not.

  On "junk" in the genome:

  http://biologos.org/blog/series/understanding-evolution-is-there-junk-in-your-genome
• 

  jgnat

  I am learning so much just by watching this thread. It was an eye-opener that so much of our genome could include false starts, redundancies, or irrelevant bits of code. I took a look at the animals and plants with the shortest genome, and I was surprised to find that complexity is not directly related to genome size.

  http://en.wikipedia.org/wiki/Genome

  We have a carnivorous plant that seems to be agressively preferring a short genome. "G. margaretae in particular may be helpful in research aimed at understanding the mechanisms behind genome downsizing."
• 

  cofty

  jgnat - That's interesting about the carnivorous plant. Most species have no mechanism for removing code from our genome. There is some evolutionary advantage in that though - it can provide spare bits of code that with future mutations could become useful.

  Our tri-colour vision is down to gene duplication with mutations.

  There are Puffer Fish that have tiny genomes of only around 400 million base pairs compared to our 3 thousand million.

  On the other hand there is an onion with 10 times as big a genome as humans.
• 

  PSacramento

  The dreaded onion !!

  Consider the onion

  One such line of evidence is that closely related species can vary widely in the amount of DNA they contain, yet have the same number of genes. For example, some species in the genus Allium (onion, garlic and related plants) can have over five times as much DNA as other species within the same group. The difference is largely in repetitive DNA sequences, such as transposons and transposon fragments. Such observations are challenging to square with the hypothesis that the species with the larger amounts require all of it for function in the strict sense, since the species in the group are all almost exactly the same structurally. If Onion Species B has five times as much DNA as Onion Species A, it does not mean that all of it is necessary to build the body form of Species B. No, the developmental process for building Species B involves laying down the very same structures that we find in Species A, with only slight modifications. So even if all of the “extra” DNA in Species B is doing something biochemically, it doesn’t mean that it is all necessary to build or maintain the body form. Furthermore, we might notice that the onion has over five times as much DNA as humans. Do we really think that it takes five times more functionally necessary DNA to build an onion than it does to make a human being? No. Much of the extra DNA, put simply, may be “functioning” in some way (i.e. biochemically active), but it is highly unlikely that it is functionally necessary. This observation led evolutionary and genome biologist T. Ryan Gregory to propose the “onion test” as a mental check against proposed universal functions for non-coding DNA (using “function” in the strict sense):

  “The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?”
• 

  sooner7nc

  I love reading "The Onion". It's where I get all my information about genome sequencing.

  Great thread guys but I'm disappointed that more members of Team Hearsvoices didn't show up for the fight.
• 

  cofty

  I'm not.

  Its like playing chess with a pigeon. It struts all over the place, shits on the board and claims victory.
• 

  frankiespeakin

  Well I'm thinkin we will have some number crunching mathematician figure out the algorithyms of life put it in a quantum computer scan you dna and make an near exact copy of you with major inprovement.

  As far as lifes common ancesty it would depend on what you would define as life? At what level makes it life. Is life the process of atoms forming into molecules or molecules with forming power over other atoms and molecules to replicate itself by a series of steps? How many repetitive processes happening all in sequence till we give it the label of life?

  I think there were other more simpler replicating molecules before dna came on the scene, rna and others before that so that I don't think any first one to reach dna level became our common ancester ,, it was happening on a much larger scale than 1,, maybe zillions all happening together.
• 

  frankiespeakin

  Junk DNA term needs changing:

  http://www.guardian.co.uk/science/2012/sep/05/genes-genome-junk-dna-encode
• 

  cofty

  Back to DNA comparisons.

  To review.... Above we made a comparison between the the protein molecule Cytochrome C in various sepcies. We saw that this ubiquitous protein is made up of around 100 amino acids and that there are more ways of assembling a Cytochrome C molecule than there are atoms in the known universe and all of them would work exactly the same - the function of a protein depends on its physical form.

  Comparison of the structure of human and chimp Cytochrome C shows that they are identical. Comparison with other species demonstrates a pattern of similarity that exactly reflects the relationships between species that was previously predicted by evolution.

  Now we can go down another layer and compare the actual DNA sequences that code for Cytochrome C.

  Remember the alphabet of DNA contains only 4 letters, A, C, G and T of which there are 3 thousand million in the human genome, divided into 23 chromosomes. The bases are read off in groups of three which gives 4^3 = 64 different words or "codons."

  Codons are chemical instructions for building amino acids and there are 20 different amino acids in the proteins of living things. This means that there are a number of different codons that will code for exactly the same amino acids.

  For any amino acid it turns out that the first 2 letters of the codon are the most important. In some cases any third letter will do and produce the same amino acid. This is referred to as codon degeneracy.

  For example the amino acid threonine will result from the codons, ACT, ACC, ACA or ACG.

  Here is a diagram of the relationship between the 64 codons and the 20 amino acids.

  

  This means that for any given protein - even if the amino acid sequence is identical - there is no reason to expect any two species to share the same nucleotide sequence. There are so many different ways of coding for the same sequence of amino acids that the numbers are impossible to comprehend. The only possible explanation for similar sequences is common ancestry.

  So back to Cytochrome C. We have said already that the amino acid sequence of humans and chimps is identical but what about the DNA sequence? There are 10^49 (ten to the power 49) different nucleotide sequences that would code for this amino acid sequence but when human and chimp genomes are compared it turns out that there is a difference of only 4 base pairs.

  Evolution tells us that the lineages leading to humans and chimps separated around 10 million years ago. The mutation rate of gene duplication is known and so it can be calculated how similar human and chimp - or any other species - genomes should be. In the case of humans and chimps that means a calculated difference of 3%. In the case of Cytochrome C we have a difference of just 1.2%.

  For every gene in the human and chimp genome there are none that differ by more than 3% exactly as evolution predicted. The same spectrum of genetic difference between species is found to be confirmed for every gene of every species examined so far.

  LINES, SINES and transposons (jumping genes) to follow...
• 

  still thinking

  Sorry, not trying to derail what you are discussing and I know this is basic...but I'm still at a basic stage with learning.

  I'm enjoying this thread so much...and cofty, you got me thinking about the egg yolk and how humans still produce the sac but not the yolk inside. And, I was reading abook to my son today that had pictures of fetuses etc..and there was a picture of the chick with what looked like an unbilical cord. So, it got me wondering. Do they have them? I thought only mammal had umbilicals connected to a placenta. And when you look at the inside of the shell, it almost looks like the way a placenta works taking nutrients from the yolk to the fetus.

  

  

  Animals have been laying eggs for millions of years; snails, fish, and many other critters produce eggs from which their young hatch. The egg of the chicken is a special kind of egg. It has a shell to help prevent drying, and a series of membranes that surround the developing chick. This kind of egg is unique to the amniotes , a group that includes turtles, lizards, birds , dinosaurs , and mammals . The last name in that list, the mammals, may have surprised you since most mammals do not lay eggs, but the earliest mammals laid eggs, and a few, such as the monotremes , still do.

  Inside the egg are a series of fluid-filled membranes which permit the embryo to survive: the amnion, allantois, yolk sac, and chorion. Surrounding and protecting the embryo is the amnion , filled with amniotic fluid , and providing the embryo with a stable fluid environment. The allantois performs two very important functions for the embryo, providing for gas diffusion, and removal of wastes. Food for the developing embryo comes from the yolk sac , which reduces in size as the embryo matures. Surrounding all the other membranes is the chorion , providing an overall enclosure for the young.

  The placenta is a "modified egg".

  In the placental mammals the membranes found in the egg have been modified somewhat. The embryo is still surrounded by an amnion filled with amniotic fluid; because it is next to and surrounds the embryo, doctors will sometimes examine the fluid to determine the health of the unborn child. The allantois and yolk sac become the umbilical cord, providing a connection through which food reaches the fetus, and wastes are removed. Together with part of the chorion, these membranes make up the placenta, which physically attaches the embryo to the uterine wall of its mother. It is across the placenta that air, food, and wastes must be transferred. Around the whole is the fluid-filled chorion, which "breaks" as labor begins.

  Monotremes were interesting...since they are mammals that lay eggs.

  Monotremes Egg-laying Mammals

  Echidna. Photo by Dr. Lloyd Glenn Ingles © 2001 California Academy of Sciences. There are only five living monotreme species: the duck-billed platypus and four species of echidna (also known as spiny anteaters). All of them are found only in Australia and New Guinea. Monotremes are not a very diverse group today, and there has not been much fossil information known until rather recently. In some ways, monotremes are very primitive for mammals because, like reptiles and birds, they lay eggs rather than having live birth. In a number of other respects, monotremes are rather derived, having highly modified snouts or beaks, and modern adult monotremes have no teeth. Like other mammals, however, monotremes have a single bone in their lower jaw, three middle ear bones, high metabolic rates, hair, and they produce milk to nourish the young.

  Im finding this all so fascinating...I just wanted to share a bit of what I had learned today...