Re: Is it possible to activate unnecessary genes in the human Chromosomes?

This is a very interesting question. Let me begin with some of the current estimates of what is in 
the human genome, and how much of it is useless.

If you compare the human genome to the genome of other organisms, it is possible to see what 
percentage of the human genome is conserved between the two species. In comparison to 
mouse, which diverged from human about 70 million years ago, about 5% of the sequence is 
conserved, meaning that there are fewer changes than one would expect over that amount of 
time if changes had no effect. About 3% of the conserved sequence is known coding sequence 
(part of the gene that codes for the amino acids of a protein sequence).

Here is an overview of one of the key mouse sequencing papers:
 http://www.bio-itworld.com/archive/021003/paperview.html

The citation is:

Mouse Genome Sequencing Consortium. "Initial sequencing and comparative analysis of the 
mouse genome." Nature 420, 520-562 (2002). 
Full text available at: www.nature.com/nature/mousegenome

Here you will find that most mouse genes (at least 99%) have a human counterpart, and about 
99% of mouse genes have a human counterpart.

Most of the rest of the human genome, the 95% that is not conserved from mouse to human, is 
repetitive "junk" DNA. These sequences are mobile genetic elements that expanded explosively 
at several distinct times in human evolution. We know this because after the repeated elements 
expand to occupy a larger percentage of the human genome, the individual copies mutate at a 
fairly constant rate over time. This means that repeats that are divergent in sequence are old, 
and repeats that are highly similar duplicated recently.

Your question implies that we can identify squid genes in the human genome that are no longer 
used by humans. A more accurate way to look at the problem is that there are a set of genes in 
common between humans and squids. There is a continuous chain of living individuals extending 
back to the common ancestor of humans and squids. Both organisms, for example, use a 
contractile apparatus consisting of actin and myosin to make their muscles work. The human and 
squid proteins differ in their sequence because the sequences in both lineages have diverged 
since these two species diverged.

If you were to look at all of the proteins expressed in gills, you would find a set of proteins 
common to cell types in the rest of the squid. There is not a single gene that says, "make a gill." 
Complex structures like hands, gills, eyes, and other organs form in response to the expression 
of an array of regulatory genes that act during development. Gills are an interesting example, 
because the gill arches of fish have become the bones of our inner ear. Here is a quote from 
Developmental Biology by Scott F. Gilbert. You can see this online at:
 http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=dbio.TOC&depth=2

__________

"One of the most celebrated cases of embryonic homology is that of the fish gill cartilage, the 
reptilian jaw, and the mammalian middle ear (reviewed in Gould 1990). First, the gill arches of 
jawless (agnathan) fishes became modified to form the jaw of the jawed fishes. In the jawless 
fishes, a series of gills opened behind the jawless mouth. When the gill slits became supported 
by cartilaginous elements, the first set of these gill supports surrounded the mouth to form the 
jaw. There is ample evidence that jaws are modified gill supports. First, both these sets of bones 
are made from neural crest cells. (Most other bones come from mesodermal tissue.) Second, 
both structures form from upper and lower bars that bend forward and are hinged in the middle. 
Third, the jaw musculature seems to be homologous to the original gill support musculature. 
Thus, the vertebrate jaw appears to be homologous to the gill arches of jawless fishes.

But the story does not end here. The upper portion of the second embryonic arch supporting the 
gill became the hyomandibular bone of jawed fishes. This element supports the skull and links 
the jaw to the cranium (Figure 1.14A). As vertebrates came up onto land, they had a new 
problem: how to hear in a medium as thin as air. The hyomandibular bone happens to be near 
the otic (ear) capsule, and bony material is excellent for transmitting sound. Thus, while still 
functioning as a cranial brace, the hyomandibular bone of the first amphibians also began 
functioning as a sound transducer (Clack 1989). As the terrestrial vertebrates altered their 
locomotion, jaw structure, and posture, the cranium became firmly attached to the rest of the 
skull and did not need the hyomandibular brace. The hyomandibular bone then seems to have 
become specialized into the stapes bone of the middle ear. What had been this bone's secondary 
function became its primary function.

The original jaw bones changed also. The first embryonic arch generates the jaw apparatus. In 
amphibians, reptiles, and birds, the posterior portion of this cartilage forms the quadrate bone of 
the upper jaw and the articular bone of the lower jaw. These bones connect to each other and are 
responsible for articulating the upper and lower jaws. However, in mammals, this articulation 
occurs at another region (the dentary and squamosal bones), thereby 'freeing' these bony 
elements to acquire new functions. The quadrate bone of the reptilian upper jaw evolved into the 
mammalian incus bone of the middle ear, and the articular bone of the reptile's lower jaw has 
become our malleus. This latter process was first described by Reichert in 1837, when he 
observed in the pig embryo that the mandible (jawbone) ossifies on the side of Meckel's 
cartilage, while the posterior region of Meckel's cartilage ossifies, detaches from the rest of the 
cartilage, and enters the region of the middle ear to become the malleus (Figure 1.14B,C). Thus, 
the middle ear bones of the mammal are homologous to the posterior lower jaw of the reptile 
and to the gill arches of agnathan fishes. Chapter 22 will detail more recent information 
concerning the relationship of development to evolution."

________

If genes are not expressed in the human genome, they do not survive intact over evolutionary 
time, because they accumulate mutations in the absence of selection. If there were squid genes 
in the human genome that could be "activated," it is likely that the accumulated mutations would 
result in a truncated gene product (3 of the 64 codons are "stop") with many changes in its 
sequence.

See also the MGI Glossary:
 http://www.informatics.jax.org/mgihome//other/glossary.shtml

Yours,

Paul Szauter
Mouse Genome Informatics