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I understand that we have 46 DNA molecules in the nucleus of our cells, arranged in 23 pairs: 22 autosomal and 1 sex chromosome pairs.
I have read in different sources that the pairs contain nearly identical members, excluding any mutations. I have also read that the pairs contain 1 member we inherited from our mothers and 1 we inherited from our fathers, which are different due to inheritance.
This seems contradictory, given that genealogical companies match up on the differences on these chromosomes.
My understanding was that meiosis creates sperm and egg cells that each carry 23 chromosomes - they are haploids. During the first steps of meiosis that creates the reproductive cells we have a combining of the parent's chromosome pair from their parents to create 4 daughter cells, each independently viable, where the recombination of the chromosome pair has occurred at somewhat predictable spots (for you perhaps :-) ) and that these spots can be related to genes. It is this step that give us our genetic variation between siblings for example. A new person's DNA is partially formed from any one of these highly varied daughter cell possibilities.
Fertilization combines the reproductive cells to produce the 46 chromosome zygote with is again diploid.
I think this understanding supports the second interpretation that our chromosome pairs are not 2 nearly identical DNA molecules but are distinct.
Have I got this right? Is there a missing process or a misunderstanding in my interpretation?
Homologous chromosomes (those that are paired up), excluding the sex pair are almost identical in size, shape and genes (members as you called them) present in them.
Genes determine traits and each homologous chromosome controls the same traits. The level of identity of a gene inside a population varies between genes. There are very conserved ones that do not change even between humans and yeast and others that vary alot event inside a species. This changes can be small in sequence length, a simple base (letter) swap or one deletion, and have a huge effect on the traits. This is how chimps and humans are very different but share 98.6% of their genome and humans are very similar and share 99.9% of their genome.
In summary, on the bigger scale homologous chromosomes are very similar (size, shape, traits inside), on the smaller scale homologous chromosomes have small changes that affect greatly.
EDIT: elaborating on when recombination occurs.
The zygote do not recombine the chromosomes it gets from it's parents. Each parent chromosomes recombine in the first step of meiosis. We do not expect them to be identifcal on the gene level (or the SNPs level). Each chromosome represent each paren't genetic material.
Lets look at parents A chromosomes
parent a Paternal: a-b-c-d-e parent b Paternal: a-B-c-D-e
parent a Maternal: a-B-C-D-e parent b Maternal: a-b-C-D-e
possible recombination (a) possible recombination (b)
(a-I) a-B-C-d-e (b-I) a-B-C-D-e
(a-II) a-b-c-D-e (b-II) a-b-c-D-e
Now the child can be any of the 4 possible combinations (and obviously all other not shown). Let's say (a-I) and (b-II). This chromosomes do not recombine until they get to the meiosis stage.
I have read in different sources that the pairs contain nearly identical members, excluding any mutations
"Nearly" is doing a lot of work there.
You have a copy of Chr 1 from your father and a copy from your mother. Your copies might have mutations as compared to your parents that happened either in you as you were developing, or in the gametes as compared to the stem cells they originated from, but most of the differences between your maternal copy and your parental copy were caused by long ago mutations that have been in your parents' families for generations, (we'd be more likely to call those polymorphisms, rather than mutations) not mutations that just happened.
Even with those differences, your two copies of Chr 1 are at least 99% identical.
Two major resources of genetic variation between siblings:
1- Random segregation of chromosomes during meiosis I. consider only mother: the mother has 46 chromosomes, 23 from grandmother and 23 from grandfather. during meiosis anaphase I, pairs of similar (homologous) chromosomes are segregated randomly. finally you have egg cells with 23 chromosomes, some from grandfather and some from grandmother. this can make 2^23 (8 millions) different combination of chromosomes for egg, and 2^23 for sperm and 2^46 (7000 billions) different combinations totally.
2- Recombination of homologous chromosomes during meiosis I. which is exchange of chromosome pieces during meiosis I metaphase, and I see you know enough about it.
Also, there are other resources of variation which are out of the level of this question.
Chapter 13: Meiosis and Sexual Life Cycles
In animals and plants, reproductive cells called GAMETES are the vehicles that transmit genes from one generation to the next.
In ASEXUAL REPRODUCTION, a single individual is the sole parent and passes copies of all its genes to its offspring without the fusion of gametes. For example, single-celled eukaryotic organisms can reproduce asexually by mitotic cell division, in which DNA is copied and allocated equally to two daughter cells. The genomes of the offspring are virtually exact copies of the parent's genome.
An individual that reproduces asexually gives rise to a CLONE, a group of genetically identical individuals. Genetic difference occasionally arise in asexually reproducing organisms as a result of changes in the DNA called mutations.
The only cells of the human body not produced by mitosis are the gametes, which develop from specialized cells called GERM CELLS in the gonads- ovaries in females and testes in males.
Plants and some species of algae exhibit a second type of life cycle called ALTERNATION OF GENERATIONS. This type includes both diploid and haploid stages that are multicellular. The multicellular diploid stage is called the sporophyte. Meiosis in the sporophyte produces haploid cells called spores. Unlike a gamete, a haploid spore doesn't fuse with another cell but divides mitotically, generating a multicellular haploid stage called the gametophyte. Cells of the gametophyte give rise to gametes by mitosis. Fusion of two haploid gametes at fertilization results in a diploid zygote, which develops into the next sporophyte generation. Therefore, in this type of life cycle, the sporophyte generation produces a gametophyte as its offspring, and the gametophyte generation produces the next sporophyte generation.
The third type of life cycle occurs in most fungi and some protists, including some algae. After gametes fuse and form a diploid zygote, meiosis occurs without a multicellular diploid offspring developing. Meiosis produces not gametes but haploid cells that then divide by mitosis and give rise to either unicellular descendants or a haploid multicellular adult organism. Subsequently, the haploid organism carries out further mitoses, producing the cells that develop into gametes. the only diploid stage found in these species is the single celled zygote.
-alternating generations, with sporophytes that grow from spores and are diploid, and gametophytes that grow from fertilized seeds and are haploid.
-Haploid phase DOES divide
-NOTE: I incorrectly told section F3 that it is only the primitive plants that alternate generations. However, that's not strictly true. All plants have a sporophyte generation, but with flowering plants it all happens within the gametophyte
In meiosis I, homologous chromosome pairs separate, creating TWO haploid daughter cells
The word chromosome ( / ˈ k r oʊ m ə ˌ s oʊ m , - ˌ z oʊ m /   ) comes from the Greek χρῶμα (chroma, "colour") and σῶμα (soma, "body"), describing their strong staining by particular dyes.  The term was coined by the German anatomist Heinrich Wilhelm Waldeyer,  referring to the term chromatin, which was introduced by Walther Flemming, the discoverer of cell division.
Some of the early karyological terms have become outdated.   For example, Chromatin (Flemming 1880) and Chromosom (Waldeyer 1888), both ascribe color to a non-colored state. 
The German scientists Schleiden,  Virchow and Bütschli were among the first scientists who recognized the structures now familiar as chromosomes. 
In a series of experiments beginning in the mid-1880s, Theodor Boveri gave definitive contributions to elucidating that chromosomes are the vectors of heredity, with two notions that became known as ‘chromosome continuity’ and ‘chromosome individuality’. 
Wilhelm Roux suggested that each chromosome carries a different genetic configuration, and Boveri was able to test and confirm this hypothesis. Aided by the rediscovery at the start of the 1900s of Gregor Mendel's earlier work, Boveri was able to point out the connection between the rules of inheritance and the behaviour of the chromosomes. Boveri influenced two generations of American cytologists: Edmund Beecher Wilson, Nettie Stevens, Walter Sutton and Theophilus Painter were all influenced by Boveri (Wilson, Stevens, and Painter actually worked with him). 
In his famous textbook The Cell in Development and Heredity, Wilson linked together the independent work of Boveri and Sutton (both around 1902) by naming the chromosome theory of inheritance the Boveri–Sutton chromosome theory (the names are sometimes reversed).  Ernst Mayr remarks that the theory was hotly contested by some famous geneticists: William Bateson, Wilhelm Johannsen, Richard Goldschmidt and T.H. Morgan, all of a rather dogmatic turn of mind. Eventually, complete proof came from chromosome maps in Morgan's own lab. 
The number of human chromosomes was published in 1923 by Theophilus Painter. By inspection through the microscope, he counted 24 pairs, which would mean 48 chromosomes. His error was copied by others and it was not until 1956 that the true number, 46, was determined by Indonesia-born cytogeneticist Joe Hin Tjio. 
The prokaryotes – bacteria and archaea – typically have a single circular chromosome, but many variations exist.  The chromosomes of most bacteria, which some authors prefer to call genophores, can range in size from only 130,000 base pairs in the endosymbiotic bacteria Candidatus Hodgkinia cicadicola  and Candidatus Tremblaya princeps,  to more than 14,000,000 base pairs in the soil-dwelling bacterium Sorangium cellulosum.  Spirochaetes of the genus Borrelia are a notable exception to this arrangement, with bacteria such as Borrelia burgdorferi, the cause of Lyme disease, containing a single linear chromosome. 
Structure in sequences Edit
Prokaryotic chromosomes have less sequence-based structure than eukaryotes. Bacteria typically have a one-point (the origin of replication) from which replication starts, whereas some archaea contain multiple replication origins.  The genes in prokaryotes are often organized in operons, and do not usually contain introns, unlike eukaryotes.
DNA packaging Edit
Prokaryotes do not possess nuclei. Instead, their DNA is organized into a structure called the nucleoid.   The nucleoid is a distinct structure and occupies a defined region of the bacterial cell. This structure is, however, dynamic and is maintained and remodeled by the actions of a range of histone-like proteins, which associate with the bacterial chromosome.  In archaea, the DNA in chromosomes is even more organized, with the DNA packaged within structures similar to eukaryotic nucleosomes.  
Certain bacteria also contain plasmids or other extrachromosomal DNA. These are circular structures in the cytoplasm that contain cellular DNA and play a role in horizontal gene transfer.  In prokaryotes (see nucleoids) and viruses,  the DNA is often densely packed and organized in the case of archaea, by homology to eukaryotic histones, and in the case of bacteria, by histone-like proteins.
Bacterial chromosomes tend to be tethered to the plasma membrane of the bacteria. In molecular biology application, this allows for its isolation from plasmid DNA by centrifugation of lysed bacteria and pelleting of the membranes (and the attached DNA).
Prokaryotic chromosomes and plasmids are, like eukaryotic DNA, generally supercoiled. The DNA must first be released into its relaxed state for access for transcription, regulation, and replication.
Each eukaryotic chromosome consists of a long linear DNA molecule associated with proteins, forming a compact complex of proteins and DNA called chromatin. Chromatin contains the vast majority of the DNA of an organism, but a small amount inherited maternally, can be found in the mitochondria. It is present in most cells, with a few exceptions, for example, red blood cells.
Histones are responsible for the first and most basic unit of chromosome organization, the nucleosome.
Eukaryotes (cells with nuclei such as those found in plants, fungi, and animals) possess multiple large linear chromosomes contained in the cell's nucleus. Each chromosome has one centromere, with one or two arms projecting from the centromere, although, under most circumstances, these arms are not visible as such. In addition, most eukaryotes have a small circular mitochondrial genome, and some eukaryotes may have additional small circular or linear cytoplasmic chromosomes.
In the nuclear chromosomes of eukaryotes, the uncondensed DNA exists in a semi-ordered structure, where it is wrapped around histones (structural proteins), forming a composite material called chromatin.
Interphase chromatin Edit
The packaging of DNA into nucleosomes causes a 10 nanometer fibre which may further condense up to 30 nm fibres  Most of the euchromatin in interphase nuclei appears to be in the form of 30-nm fibers.  Chromatin structure is the more decondensed state, i.e. the 10-nm conformation allows transcription. 
During interphase (the period of the cell cycle where the cell is not dividing), two types of chromatin can be distinguished:
- , which consists of DNA that is active, e.g., being expressed as protein. , which consists of mostly inactive DNA. It seems to serve structural purposes during the chromosomal stages. Heterochromatin can be further distinguished into two types:
- Constitutive heterochromatin, which is never expressed. It is located around the centromere and usually contains repetitive sequences.
- Facultative heterochromatin, which is sometimes expressed.
Metaphase chromatin and division Edit
In the early stages of mitosis or meiosis (cell division), the chromatin double helix become more and more condensed. They cease to function as accessible genetic material (transcription stops) and become a compact transportable form. The loops of 30-nm chromatin fibers are thought to fold upon themselves further to form the compact metaphase chromosomes of mitotic cells. The DNA is thus condensed about 10,000 fold. 
The chromosome scaffold, which is made of proteins such as condensin, TOP2A and KIF4,  plays an important role in holding the chromatin into compact chromosomes. Loops of 30 nm structure further condense with scaffold into higher order structures. 
This highly compact form makes the individual chromosomes visible, and they form the classic four arm structure, a pair of sister chromatids attached to each other at the centromere. The shorter arms are called p arms (from the French petit, small) and the longer arms are called q arms (q follows p in the Latin alphabet q-g "grande" alternatively it is sometimes said q is short for queue meaning tail in French  ). This is the only natural context in which individual chromosomes are visible with an optical microscope.
Mitotic metaphase chromosomes are best described by a linearly organized longitudinally compressed array of consecutive chromatin loops. 
During mitosis, microtubules grow from centrosomes located at opposite ends of the cell and also attach to the centromere at specialized structures called kinetochores, one of which is present on each sister chromatid. A special DNA base sequence in the region of the kinetochores provides, along with special proteins, longer-lasting attachment in this region. The microtubules then pull the chromatids apart toward the centrosomes, so that each daughter cell inherits one set of chromatids. Once the cells have divided, the chromatids are uncoiled and DNA can again be transcribed. In spite of their appearance, chromosomes are structurally highly condensed, which enables these giant DNA structures to be contained within a cell nucleus.
Human chromosomes Edit
Chromosomes in humans can be divided into two types: autosomes (body chromosome(s)) and allosome (sex chromosome(s)). Certain genetic traits are linked to a person's sex and are passed on through the sex chromosomes. The autosomes contain the rest of the genetic hereditary information. All act in the same way during cell division. Human cells have 23 pairs of chromosomes (22 pairs of autosomes and one pair of sex chromosomes), giving a total of 46 per cell. In addition to these, human cells have many hundreds of copies of the mitochondrial genome. Sequencing of the human genome has provided a great deal of information about each of the chromosomes. Below is a table compiling statistics for the chromosomes, based on the Sanger Institute's human genome information in the Vertebrate Genome Annotation (VEGA) database.  Number of genes is an estimate, as it is in part based on gene predictions. Total chromosome length is an estimate as well, based on the estimated size of unsequenced heterochromatin regions.
|Chromosome||Genes ||Total base pairs||% of bases||Sequenced base pairs ||% sequenced base pairs|
|X (sex chromosome)||800||154,913,754||5.0||151,058,754||97.51%|
|Y (sex chromosome)||200 ||57,741,652||1.9||25,121,652||43.51%|
In eukaryotes Edit
These tables give the total number of chromosomes (including sex chromosomes) in a cell nucleus. For example, most eukaryotes are diploid, like humans who have 22 different types of autosomes, each present as two homologous pairs, and two sex chromosomes. This gives 46 chromosomes in total. Other organisms have more than two copies of their chromosome types, such as bread wheat, which is hexaploid and has six copies of seven different chromosome types – 42 chromosomes in total.
Normal members of a particular eukaryotic species all have the same number of nuclear chromosomes (see the table). Other eukaryotic chromosomes, i.e., mitochondrial and plasmid-like small chromosomes, are much more variable in number, and there may be thousands of copies per cell.
Asexually reproducing species have one set of chromosomes that are the same in all body cells. However, asexual species can be either haploid or diploid.
Sexually reproducing species have somatic cells (body cells), which are diploid [2n] having two sets of chromosomes (23 pairs in humans), one set from the mother and one from the father. Gametes, reproductive cells, are haploid [n]: They have one set of chromosomes. Gametes are produced by meiosis of a diploid germ line cell. During meiosis, the matching chromosomes of father and mother can exchange small parts of themselves (crossover), and thus create new chromosomes that are not inherited solely from either parent. When a male and a female gamete merge (fertilization), a new diploid organism is formed.
Some animal and plant species are polyploid [Xn]: They have more than two sets of homologous chromosomes. Plants important in agriculture such as tobacco or wheat are often polyploid, compared to their ancestral species. Wheat has a haploid number of seven chromosomes, still seen in some cultivars as well as the wild progenitors. The more-common pasta and bread wheat types are polyploid, having 28 (tetraploid) and 42 (hexaploid) chromosomes, compared to the 14 (diploid) chromosomes in the wild wheat. 
In prokaryotes Edit
Prokaryote species generally have one copy of each major chromosome, but most cells can easily survive with multiple copies.  For example, Buchnera, a symbiont of aphids has multiple copies of its chromosome, ranging from 10–400 copies per cell.  However, in some large bacteria, such as Epulopiscium fishelsoni up to 100,000 copies of the chromosome can be present.  Plasmids and plasmid-like small chromosomes are, as in eukaryotes, highly variable in copy number. The number of plasmids in the cell is almost entirely determined by the rate of division of the plasmid – fast division causes high copy number.
In general, the karyotype is the characteristic chromosome complement of a eukaryote species.  The preparation and study of karyotypes is part of cytogenetics.
Although the replication and transcription of DNA is highly standardized in eukaryotes, the same cannot be said for their karyotypes, which are often highly variable. There may be variation between species in chromosome number and in detailed organization. In some cases, there is significant variation within species. Often there is:
1. variation between the two sexes 2. variation between the germ-line and soma (between gametes and the rest of the body) 3. variation between members of a population, due to balanced genetic polymorphism 4. geographical variation between races 5. mosaics or otherwise abnormal individuals.
Also, variation in karyotype may occur during development from the fertilized egg.
The technique of determining the karyotype is usually called karyotyping. Cells can be locked part-way through division (in metaphase) in vitro (in a reaction vial) with colchicine. These cells are then stained, photographed, and arranged into a karyogram, with the set of chromosomes arranged, autosomes in order of length, and sex chromosomes (here X/Y) at the end.
Like many sexually reproducing species, humans have special gonosomes (sex chromosomes, in contrast to autosomes). These are XX in females and XY in males.
History and analysis techniques Edit
Investigation into the human karyotype took many years to settle the most basic question: How many chromosomes does a normal diploid human cell contain? In 1912, Hans von Winiwarter reported 47 chromosomes in spermatogonia and 48 in oogonia, concluding an XX/XO sex determination mechanism.  Painter in 1922 was not certain whether the diploid number of man is 46 or 48, at first favouring 46.  He revised his opinion later from 46 to 48, and he correctly insisted on humans having an XX/XY system. 
New techniques were needed to definitively solve the problem:
- Using cells in culture
- Arresting mitosis in metaphase by a solution of colchicine
- Pretreating cells in a hypotonic solution 0.075 M KCl, which swells them and spreads the chromosomes
- Squashing the preparation on the slide forcing the chromosomes into a single plane
- Cutting up a photomicrograph and arranging the result into an indisputable karyogram.
It took until 1954 before the human diploid number was confirmed as 46.   Considering the techniques of Winiwarter and Painter, their results were quite remarkable.  Chimpanzees, the closest living relatives to modern humans, have 48 chromosomes as do the other great apes: in humans two chromosomes fused to form chromosome 2.
Chromosomal aberrations are disruptions in the normal chromosomal content of a cell and are a major cause of genetic conditions in humans, such as Down syndrome, although most aberrations have little to no effect. Some chromosome abnormalities do not cause disease in carriers, such as translocations, or chromosomal inversions, although they may lead to a higher chance of bearing a child with a chromosome disorder. Abnormal numbers of chromosomes or chromosome sets, called aneuploidy, may be lethal or may give rise to genetic disorders.  Genetic counseling is offered for families that may carry a chromosome rearrangement.
The gain or loss of DNA from chromosomes can lead to a variety of genetic disorders. Human examples include:
- , which is caused by the deletion of part of the short arm of chromosome 5. "Cri du chat" means "cry of the cat" in French the condition was so-named because affected babies make high-pitched cries that sound like those of a cat. Affected individuals have wide-set eyes, a small head and jaw, moderate to severe mental health problems, and are very short. , the most common trisomy, usually caused by an extra copy of chromosome 21 (trisomy 21). Characteristics include decreased muscle tone, stockier build, asymmetrical skull, slanting eyes and mild to moderate developmental disability.  , or trisomy-18, the second most common trisomy.  Symptoms include motor retardation, developmental disability and numerous congenital anomalies causing serious health problems. Ninety percent of those affected die in infancy. They have characteristic clenched hands and overlapping fingers. , also called idic(15), partial tetrasomy 15q, or inverted duplication 15 (inv dup 15). , which is very rare. It is also called the terminal 11q deletion disorder.  Those affected have normal intelligence or mild developmental disability, with poor expressive language skills. Most have a bleeding disorder called Paris-Trousseau syndrome. (XXY). Men with Klinefelter syndrome are usually sterile and tend to be taller and have longer arms and legs than their peers. Boys with the syndrome are often shy and quiet and have a higher incidence of speech delay and dyslexia. Without testosterone treatment, some may develop gynecomastia during puberty. , also called D-Syndrome or trisomy-13. Symptoms are somewhat similar to those of trisomy-18, without the characteristic folded hand. . This means there is an extra, abnormal chromosome. Features depend on the origin of the extra genetic material. Cat-eye syndrome and isodicentric chromosome 15 syndrome (or Idic15) are both caused by a supernumerary marker chromosome, as is Pallister–Killian syndrome. (XXX). XXX girls tend to be tall and thin and have a higher incidence of dyslexia. (X instead of XX or XY). In Turner syndrome, female sexual characteristics are present but underdeveloped. Females with Turner syndrome often have a short stature, low hairline, abnormal eye features and bone development and a "caved-in" appearance to the chest. , which is caused by partial deletion of the short arm of chromosome 4. It is characterized by growth retardation, delayed motor skills development, "Greek Helmet" facial features, and mild to profound mental health problems. . XYY boys are usually taller than their siblings. Like XXY boys and XXX girls, they are more likely to have learning difficulties.
Sperm aneuploidy Edit
Exposure of males to certain lifestyle, environmental and/or occupational hazards may increase the risk of aneuploid spermatozoa.  In particular, risk of aneuploidy is increased by tobacco smoking,   and occupational exposure to benzene,  insecticides,   and perfluorinated compounds.  Increased aneuploidy is often associated with increased DNA damage in spermatozoa.
Chromosomes of Pacific hydrothermal vent invertebrates: towards a greater understanding of the relationship between chromosome and molecular evolution
Karyotypes for several East Pacific Rise hydrothermal vent invertebrates are described here for the first time: the vestimentiferans Riftia pachyptila and Oasisia alvinae , the alvinellid polychaetes Alvinella pompejana, A. caudata and Paralvinella grasslei , the polynoid polychaetes Branchinotogluma grasslei and Branchipolynoe symmytilida , the serpulid Laminatubus alvini and the mytilid bivalve Bathymodiolus thermophilus . For comparative purposes, the karyotype of the Atlantic vent mussel Bathymodiolus azoricus is also described here for the first time. Each species has its own unique chromosomal characteristics which can be interpreted both in terms of group characteristics and species divergence. From comparisons with published results on other vent species and closely-related coastal species, we identified a positive correlation between chromosome number variation and molecular divergence at two ribosomal ribonucleic acid gene loci (the 18S and 28S rRNA). Whilst the patterns of chromosome divergence we found were generally within the ranges previously reported for these taxonomic groupings, there was an apparent inconsistency in the case of Branchipolynoe symmytilida (EPR) and Branchipolynoe seepensis (MAR), which show a greater degree of divergence at the chromosome level compared with other members of the same genus. Moreover, polychaetes as a whole showed greater variation in the number and structural divergence of chromosomes compared to Mytilids (structural information only). Our findings highlight the great potential for chromosome analysis in future taxonomic and evolutionary studies of the deep-sea vent fauna.
I. From Whom: Ape-like Primates or Fully Human People?
When considering human origins, the most natural place to start is on the question of whether humans have an ape-like ancestry. Before we can discuss the minutiae of the genetics of the human race, we need to ask whether our race is indeed human or whether we are simply highly evolved primates. Ever since Darwin, evolutionists have claimed that apes represent our closest living biological relatives.4 Evolutionary creationists (a.k.a. theistic evolutionists) agree and expect to find unequivocal genetic evidence of a common genealogical heritage between mankind and the orangutans, gorillas, and chimpanzees. Current evolutionary literature identifies the chimpanzee as the closest living relative of humans, and evolutionists place the split between these two lineages (from a common ape-like ancestor, not a chimpanzee) about 3 million to 13 million years ago.5
In contrast, a plain reading of Scripture reveals a starkly different narrative on human ancestry. As has been argued in an earlier chapter, Genesis 1–2 teaches that God created man in His own image, categorically distinct from any animals, and that He did so supernaturally by forming Adam from the dust and Eve from Adam’s side. Human evolution from pre-existing ape-like creatures is not compatible with the Genesis narrative.
Furthermore, the rest of Scripture identifies Adam and Eve as the sole progenitors of the entire human race, and Noah, his wife, his three sons, and their wives as the most immediate ancestors of modern humans.6 Shortly after the global Flood of Noah’s day, the human ancestors of the modern “races”7 or ethnic groups formed as a result of the confusion of languages at Babel (Gen 11:8–9).8 Apes as precursors to humans do not enter the picture under the creation view.
Because of the nature of the genetic discussion that follows, the time element of creation is also critical to the ancestry question. Under the young-earth creation (YEC) view, Adam and Eve were created approximately 6,000 years ago, and the global Flood of Noah and the population bottleneck that followed occurred about 4,500 years ago. The Tower of Babel incident followed shortly (i.e., a couple centuries) after the Flood.9
These two strikingly different accounts — evolution and YEC — for the origin of humans lead to very different expectations about the genetics of modern humans and apes. In some cases, however, the expectations are obviously the same. For instance, from an anatomical perspective, great apes are the most similar creatures to humans, and both sides can make a general prediction that, from a genetic perspective, apes should be the most similar to humans. While humans share different levels and traits of morphological similarity with gorillas, orangutans, and chimpanzees that don’t seem to indicate any clear evolutionary pattern, the current evolutionary consensus is that humans should be most similar to chimpanzees genetically — although this widely accepted paradigm has recently been disputed based on analyses of morphological traits by several evolutionists who claim that orangutans are the closest human relative.10
As another example, both models accept the science of empirical genetic discovery. Hence, to claim that the existence of the basic science of genetics somehow validates one model over the other would be erroneous — a type-3 experiment that fails to distinguish among the competing ideas in question. Therefore, it is essential to clearly identify the specific predictions of each model in order to distinguish which genetic data actually constitute a type-1 experiment (e.g., one that differentiates YEC from evolution ) and which constitute lesser types of experiments.
Are Humans 99% Genetically Identical to Chimpanzees?
One common example of a type-2 experiment is predicting the genetic difference between humans and chimpanzees. The evolutionary model has very specific expectations about this figure, and a discrepancy between predictions and facts should result in the rejection of the evolutionary hypothesis. However, since the YEC model does not make specific predictions about human-ape genetic differences, a match between evolutionary expectations and scientific fact would not inform the origins debate (i.e., would not be decisive in evolution ’s favor).
But the silence of the YEC model on human-chimp genetic differences is not a weakness of the model. We could just as well challenge the evolutionists to predict the number of animals that were taken on board Noah’s ark. This request would be fruitless and irrelevant to the debate since a global Flood and an ark are not part of the evolutionary model. However, if the YEC model failed to predict the numbers on board the ark accurately, then we would need to reevaluate aspects of the YEC model. Conversely, since human-ape ancestry is not part of the YEC model, the actual number of genetic differences between humans and chimpanzees is, at best, a type-2 experiment for testing the claim that humans descended from ape-like creatures — successful evolutionary predictions would not vindicate evolution in the origins debate, while evolutionary predictive failures could be grounds to reject the evolutionary view.
With these experimental parameters in mind, we can now investigate the actual human-chimp genetic comparison in depth. If we think of genetic inheritance as analogous to copying the text of a book, the process of passing on genetic information from one generation to the next is similar to the process of transcribing the text of a book. To make the analogy tighter, inheritance is like copying the text of a book without having a perfect spell checker,11 and then using the corrupted copy as the template for the next round of copying.
Biologically, the text of the genetic book is contained in a chemical substance called DNA. The DNA in our cells is, in essence, a chemical instruction manual for building and maintaining our anatomy and physiology from conception to death. The actual instructions are encoded in a 4-letter chemical alphabet, and the combination of these letters into chemical “words” and “sentences” carries biological meaning. In total, the DNA in our cells is billions of letters long — a very large biological “book.”
When DNA is copied in sperm and egg cells prior to conception, the copying process is imperfect. The rate of copying mistakes (called mutations) has been measured in both humans and chimpanzees, and the rates are fairly similar. About 60 mutations happen each generation.12
Using rounded numbers, if the human and chimpanzee lineages split 3–13 million years ago, and if the years from one generation to the next are about 20 years, then 150,000–650,000 generations have passed since the two species last shared a common ancestor.13 In each lineage, about 60 DNA mutations happen in each of those hundreds of thousands of generations leading to an expectation that the DNA of humans and the DNA of chimpanzees should differ by about 18–80 million DNA letters.14
Thinking of DNA again like a book, we can measure book sizes by their word count, and if we wanted to be very technical, we could measure it by the total letter count. Since the total letter count in humans and chimpanzees is around 3 billion DNA letters,15 evolutionists expect about a 1–3% genetic (DNA) difference between these two species today.16
The actual difference is about 12% — a number that is about ten times higher than the predicted value.17 Though the scientist responsible for identifying this fact is a young-earth creationist, this discovery is not the result of creationist manipulation of data to fit a pre-determined conclusion. If you read the fine print in the original evolutionary publication that announced the determination of the chimpanzee DNA sequence, you can reach a similar conclusion.18 Humans and chimpanzees are not 99% identical. They are only 88% identical, which means that the two species differ by nearly 400 million (400,000,000) DNA letters!19
Thus, the question of human-chimpanzee DNA differences offers no assistance to the evolutionary model on at least three counts. First, whatever the difference is, it cannot falsify the YEC model, making it a type-2 experiment at best. Second, current evolutionary predictions for the human-chimp genetic difference fail to account for the gigantic genetic gap between these two species.
Third, the evolutionary prediction of a 1% difference isn’t really a prediction at all. The evolutionary time at which the human and chimpanzee lineages split has been revised to fit the genetic data. Earlier predictions for the time of divergence for these species were originally in the 3 to 6 million year range,20 and the measurement of the DNA copying error rate in chimpanzees caused some investigators to (controversially) bump the time back further to
13 million years.21 Thus, the absolute difference between humans and chimpanzees isn’t a confirmed prediction as much as it is a post hoc retrofitting of predictions to facts.
These evolutionary problems aside, we are still left with the question of how to evaluate the YEC model on the human ancestry question. If human-ape genetic differences do not test validity of the YEC model of human origins, what experiment can? What genetic expectations follow from the specific YEC narrative?
In short, the answer is that, if YEC is correct, then YE creationists should be able to explain human-human DNA differences and ape-ape DNA differences [as opposed to human-ape DNA differences] without any need to reference or invoke common ancestry. In other words, YE creationists make predictions for genetic differences among individuals that share a common ancestor under the YEC view (i.e., all humans), not for individuals that were created separately (i.e., humans and apes), and these predictions can be compared to the genetic facts.
If genetic data matched these YEC expectations, would this result require rejection of the evolutionary model? Since evolutionists have spent years refining their own ideas about human-human and ape-ape genetic differences (and also believe that special creation as an alternative is unacceptable), this result would probably do nothing to settle the debate about human origins. In essence, it would be another example of a type-2 experiment — if the results are inconsistent with the YEC expectations, then perhaps the scientific elements of the YEC model should be reevaluated. But if the results confirm the YEC expectations, this discovery would probably do little to change the evolutionary claims about human-ape common ancestry.
Since subsequent sections will explore this question further, the major remaining question in this section is whether the claimed evolutionary evidences for human-ape ancestry are valid type-1 experiments. The evidences listed on the BioLogos website are presented as such — as being unequivocal proof of common ancestry and as very inconsistent with the YEC view. The evidences in the mainstream scientific literature assume the same. But is the claim true?
Relative Genetic Patterns/Nested Hierarchies
Nearly every single one of the evidences presented by BioLogos and mainstream geneticists represents a type-3 experiment or, at best, type-2. For example, one of the most common evidences cited in favor of an ape ancestry in the human lineage is the relative pattern of genetic differences between humans and apes, and between humans and other species. In short, evolutionists expect natural selection to produce a branching, tree-like pattern of genealogical relationships among the living species on this planet.22 They further expect that, if humans arose via the process of natural selection from an ape-like ancestor, then genetic comparisons among humans, apes, and other species should reveal a branching, tree-like pattern as well.
This expectation contrasts to the expectation about the percent DNA differences between humans and chimpanzees that we discussed earlier. The earlier expectation was a quantitative prediction the current expectation is a qualitative prediction. That is, qualitatively, if humans have ancestry prior to the first Homo sapiens, then evolutionists expect humans to be relatively close genetically to the great apes, then slightly less close genetically to the rest of the primates, then even less similar genetically to other mammals, and quite different genetically from invertebrates and plants. To be clear, the absolute number of differences is not so critical as long as the same relative pattern (in this case, a nested hierarchical pattern) holds true.
For this argument to carry any scientific weight as a type-1 experiment in support of evolution , the YEC model would need to predict a different pattern. Otherwise, this argument would represent another type-3 experiment — useless to the overall origins debate.
However, it doesn’t take much reflection to see that YEC and evolution make the same prediction about the relative genetic hierarchies found in nature. Under the YEC model, God designed the entire universe, including the various kinds of biological life that exist in it, and we would expect to find that life fits a design pattern. Since humans are made in God’s image, we can get a sense for what kinds of design patterns God might have used by examining the patterns that result from human designs. Examples of nested hierarchies abound among the designed things in our world.
For example, designed means of transportation easily fit a relative hierarchical pattern. This fact is unequivocal. Sedans resemble SUVs more than they resemble tractor trailers, and all three vehicles have more in common than do sedans and amphibious assault vehicles. The latter two vehicles have more in common with one another than with submarines, and this simple pattern matches the type of hierarchy that we see in biology.23
Therefore, nested hierarchical patterns are as much the expectation of the YEC view as they are of the evolutionary view. The relative hierarchy of genetic differences among humans, great apes, mammals, and invertebrates fits the YEC model at least as well as the evolutionary one. So, to claim nested hierarchical patterns in the biological world as exclusive evidence of evolution would be analogous to claiming that the existence of people proves YEC. Neither claim constitutes a legitimate scientific experiment. Both are type-3 experiments and, therefore, reveal nothing about the validity of either view, despite the confident claims of evolutionists to the contrary.24
While these two examples (absolute and relative genetic differences between humans and the apes) do not constitute an exhaustive review of all the claimed genetic evidences for human-ape ancestry, they represent some of the most prominent, and they illustrate the Achilles’ heels of the remaining ones — failure to satisfy the requirements of a type-1 experiment.
Human Chromosome 2 Fusion?
Consider another example. If we return to our book analogy, just as the text of a book is broken up into chapters, so also the billions of letters in the DNA code for humans and chimpanzees are broken up into major divisions called chromosomes. However, because DNA comes from each parent, these chromosomes come in pairs.
Evolutionists have claimed for years that the human chromosome pair number 2 is actually an accidental fusion of two pairs of ancestral chromosomes inherited from ape-like creatures.25 In short, they claim that the human-chimp ancestor had 48 chromosomes. Today, humans have 46. Since chromosomes come in two copies — e.g., the ape-like ancestor would have had 2 pairs of 24 chromosomes, and humans today have 23 pairs of chromosomes — and since humans have fewer total chromosomes than apes, evolutionists claim that one of the ancestral pairs of chromosomes fused to another ancestral pair of chromosomes. This would reduce the total chromosomes count from 48 to 46.26
Since the YEC view makes no overt predictions about the differences between humans and chimpanzees in DNA organization or in the structure of DNA, the existence of a chromosome fusion would not have said anything relevant to the human origins debate. However, in this case evolutionists also made their claim prematurely, before all the evidence was acquired. Effectively, the evolutionary claims about the structure of human chromosome 2 represented a prediction rather than an observation.
Recent reanalysis of human chromosome 2 has contradicted this evolutionary prediction. No evidence for a fusion exists. In fact, the alleged site where the fusion supposedly took place actually represents a highly organized, functional gene (in our analogy, think of genes as words or sentences).27 Thus, starting from the assumption of human-ape common ancestry, evolutionists have actually made a failed prediction about the structure and function of DNA within our cells.
The failed evolutionary prediction on chromosome function extends beyond the purported fusion site. The BioLogos community has claimed that overall arrangement of DNA along chromosomes among humans and the great apes is inexplicable apart from common ancestry: “There is no good biological reason to find the same genes in the same order in unrelated organisms, and every good reason to expect very different gene orders.”28
Do evolutionists actually have a large body of experimental results demonstrating “no good biological reason to find the same genes in the same order in unrelated organisms”? In the few cases where functional analyses have been performed, the results contradict this evolutionary assertion. The chromosomal context in which genes find themselves appears to play a significant role in how the genes function.29 In fact, human-designed computer code must also follow specific formats and contextual guidelines as well. So our previous analogy of human-designed systems as we applied to the idea of hierarchy holds true here as well. Thus, whether applied to predicted DNA differences or DNA function, the evolutionary model of common ancestry has not been vindicated.
Conversely, the prediction of function is actually one of the few arenas in the question of human ancestry in which a type-1 experiment could be conducted. Evolutionists and creationists make very different predictions about the function of the billions of DNA letters in the human sequence, and experiments testing function would clearly distinguish which model makes better predictions, as we demonstrate below.
Shared Genetic “Mistakes”?
To make the point from a different angle, the members of BioLogos have made a host of claims on their website about shared “pseudogenes” and other types of purported shared biological “mistakes” in apes and humans. In fact, two of the three main “facts” that the website lists as genetic evidence for human evolution involve an implicit statement about function.30 In reality, hardly any actual experiments have been performed on the billions of DNA letters in humans and chimpanzees. “Pseudogene” actually represents a premature label for a particular segment of DNA that resembles a broken gene but which had never been experimentally tested for function. Thus, virtually all claims that BioLogos and other evolutionists have made about genetic “mistakes” are not arguments for evolution but bald assertions without a basis in experimental fact. Technically, this would make these arguments pseudoscience. However, for the sake of discussion, we’re willing to entertain these claims as predictions stemming from the assumption that evolution is true.
Conversely, from the assumptions about human ancestry inherent to the YEC model, creationists have published a testable, predictive model of genetic function31 (see references for details). For the particular DNA differences that we examined, we expect them to function in each organism’s respective biology, whereas the evolutionary model claims that these particular DNA sequences are functionally neutral and are a reflection, therefore, of ancestry alone. Since precious few experiments have actually been done on genetic function, we now have a basis for doing a type-1 experiment in the future. By experimentally changing these sequences, we can evaluate whether or not these differences are functional — and confirm or reject the predictions of each origins model.
For other DNA sequences, a few experiments have been performed, and the trajectory is not looking good for evolution. For example, after the human DNA sequence was elucidated in 2001, it was widely proclaimed that the vast majority of our billions of DNA letters were useless, non-functional leftovers of our evolutionary heritage and therefore called “junk” DNA.32 However, scientists didn’t actually do any experimental tests on the billions of letters until the Encyclopedia of DNA Elements (ENCODE) project was initiated in 2003. The first tier of ENCODE only examined about 1% of the human genome as an initial test, and they found preliminary evidence for pervasive function for the vast majority of those billions of letters.33 Then after extending this type of research to the entire human genome, using mostly human cell lines (not fresh tissues from living humans) they reported in 2012 that at least 80% of the genome had significant levels of biochemical function.34 It wasn’t useless junk after all.
Many new discoveries in recent years are now pushing this level of functionality even higher. The leader of the ENCODE project, Ewan Birney, is predicting that the human genome will soon prove to be 100% functional.35 Needless to say, the traditional neo-Darwinian evolutionists outside the practical biomedical genetics community of ENCODE are outraged that the data is not supporting their dogmatic evolutionary claims.36
In addition to these genome-wide results, other studies focusing on specific examples of “poster child” evolutionary pseudogenes regularly damage the credibility of the evolutionary claims. For example, the beta-globin pseudogene has obvious evidence for function,37 and one of the favorite pseudogene examples (e.g., vitellogenin) of the BioLogos geneticist, Dennis Venema, can also no longer be labeled a non-functional relic.
Specifically, Venema claimed, “Humans have the remains of a gene devoted to egg yolk production in our DNA in exactly the place that evolution would predict.”38 But recent research has exposed this as nearly impossible to reconcile with the facts.39 The supposed evidence for this “egg yolk” gene is so pitiful that it’s hard to imagine how anyone could have seriously entertained this hypothesis in the first place. It’s like identifying the letter “e” in the Bible, finding the same letter in Darwin’s On the Origin of Species, and then claiming that the books were modified from a common ancestor — you really have to stretch your imagination to accept this claim. Conversely, there is so little DNA remnant of the egg yolk gene that it requires a real strain of the imagination to see why some evolutionists pursued this line of reasoning in the first place. Current data suggest that they mistook a functional DNA sequence (enhancer element) inside a genomic address messenger gene involved with brain tissue function, for a non-functional egg yolk gene “remnant.”40 Not surprisingly, the BioLogos community has downplayed the significance of these accumulating discoveries and tried to turn the tables on creationists with clever rhetorical games. Rather than admit the obvious damaging implications for evolution,41 the BioLogos staff has turned the argument around and challenged creationists to explain the remaining data that BioLogos claimed demonstrated non-function.41 In fact, Dennis Venema recently went so far as to claim, “Having the complete genome sequences for a variety of great apes makes looking for additional shared mutations a trivial exercise, and it is no exaggeration to say that there are thousands of examples that could be used.”42
But the BioLogos rejoinder misses the big picture and the point. First, preliminary biochemical evidence for function does not exist merely for the two examples of pseudogenes that we discussed. It exists for at least 80% of all the pseudogenes in humans.
80% of all the pseudogenes in humans.43 And the other 20% may still yet be found to be functional in some human tissue or under some physiological condition yet to be studied . . . and there are many. That’s the catch: many noncoding RNA genes (like pseudogenes) are only expressed under certain conditions.
Second, challenging creationists to explain the remaining examples of “non-function” assumes that actual experiments have been performed that demonstrate non-function. They have not. The reality is that we have only just begun to uncover the functionality of the human genome. Consider just how many experiments would need to be performed to conclude with any sort of confidence that a particular set of DNA sequences has zero function. The number of possible scenarios in which a DNA sequence might plausibly function is now proving to be enormous. For example, in the short nine-month window of time that represents human embryonic development, a single cell turns into a fully formed baby that contains hundreds of cell types that must execute an unimaginable number of cellular tasks. Surely the developing baby calls upon enormous swaths of DNA code to execute this developmental program — and then silences or repurposes them for the remainder of its life via another type of code (a code which is being studied by investigators in a scientific field termed “epigenetics”).44 The dynamic use of DNA sequence during development is very different than the vast majority of DNA sequence use in the adult. Experimentally testing a DNA sequence during each of these unique windows of time in which sections of DNA are used and then silenced would be an enormous (and morally questionable) experiment. However, expressed RNA sequences have been analyzed in organ donors, aborted fetal tissue, and embryonic stem cells, with the latter two involving the murder of innocent babies. Nevertheless, these morbid data have only served to increase the known functionality and complexity of the human genome. In addition, until experiments are performed in living humans, which is also unethical, it is both inappropriate and scientifically uninformed to claim “non-function” for human DNA. In short, the recent decade of experimental results on human DNA sequences that demonstrate biochemical evidence for function are just the beginning of our understanding as to the complexity and function of the genome. Perhaps the most important point that can be taken from all this is the trajectory of these results — we watched the scientific community go from claiming high levels of non-function in the early 2000s to claiming evidence for nearly pervasive function just a decade later. This suggests that more experiments will only increase the percentage of human DNA sequence that performs a biological function just as the current leader of the ENCODE project is predicting. This upward trajectory does not bode well for evolution , a fact that the BioLogos community is very reticent to admit.
On a side note, related to the question of human-ape ancestry is the question of the relationships between Neanderthals and modern humans. Interestingly, most people would be surprised to know that evolutionists consider Neanderthals to be fully human, hence they are given the technical name “archaic humans” as opposed to modern contemporary humans. An increasing number of publications claim to have recovered DNA from ancient human or human-like samples, and the comparison of these DNA samples with those of modern humans could inform the ancestry question.
Though YEC advocates and evolutionists both agree that modern humans and Neanderthals had a common ancestor (YE creationists would say that Neanderthals are post-Flood descendants of Adam and Eve), these two positions disagree on when the Neanderthals lived — tens to hundreds of thousands of years ago (evolutionary model) versus about 4,500 years or less (YEC model). Evidence for a prehistoric45 human population could add credence to the evolutionary claim that human ancestry stretches far back in time — so far back that it touches on the boundaries of an alleged divergence from an ape lineage. Time is the magical key to the evolutionary equation, despite the fact that no viable human-ape transitional forms exist in the fossil record, as discussed in a separate chapter.
Without going into great technical detail, the short answer to the question of what Neanderthal DNA implies regarding the origins issue is that Neanderthal and ancient DNA samples appear to be too degraded and often untrustworthy for use in rigorous genetic analyses. In addition, analyses are perpetually plagued with DNA contamination from microorganisms and modern human DNA from lab workers.46 Finally, no one knows the rate at which Neanderthal DNA changes from generation to generation — and it might change at a rate much faster than that reported for modern human individuals.47
As things stand now, the most credible research comparing Neanderthals to modern humans merely shows that their DNA is human. The dating of the bones from the sites in which Neanderthals are found are not based on DNA, but other types of spurious data, and the evolutionists are constantly changing the dates of the material found in these locations — a fact in and of itself that shows how subjective the whole process really is.
To summarize, on the question of human-ape common ancestry, all of the claimed evolutionary evidences are type-2 or type-3 experiments that fail to eliminate the main competing hypothesis, YEC (Table 2). Instead of being a minor side issue in the bigger human ancestry debate, this very poor scientific track record for evolution represents a systematic failure across the board. In nearly every type of genetic comparison that can be performed between humans and chimpanzees, the evolutionary model has made erroneous predictions (Table 3).
|Evolutionary Claim||Actual Data||Type of Experiment|
|Human-chimpanzee genetic identity is 98-99%||Actual genetic identity is only 88% (i.e., 400,000,000 DNA differences exist between the two species)||2|
|Humans are genetically closer to apes than to other animal species, unequivocally demonstrating common ancestry||Relative hierarchies are characteristics of design||3|
|Human chromosome #2 arose via fusion of two ape-like chromosomes||The purported “fusion” site is actually a functional DNA element in a human gene||2|
|Gene order along chromosomes has no function, therefore shared gene order demonstrates common ancestry||Gene order along chromosomes does indeed perform a function||2|
|Humans and chimpanzees shared genetic mistakes (e.g., pseudogenes)||Pseudogenes appear to be functional DNA elements, not mistakes||2|
|Humans possess the broken remnants of an ancient chicken gene (vitellogenin)||No such remnant exists instead the “fragment” appears to be a functional DNA element||2|
|Type of Genetic Comparison/Analysis||Evolutionary Success or Failure?|
|Total DNA differences between humans and chimpanzees||Failure to predict total genetic differences (a big genetic gap separates the two species)|
|Relative genetic differences between humans and chimpanzees||Irrelevant to debate (evolutionary comparison fails to refute the YEC model, thereby making it scientifically invalid)|
|Chromosome differences between humans and chimpanzees||Failure to predict chromosome differences (no evidence for claimed fusion event)|
|Total genetic function in humans||Current scientific trajectory points toward much more function than predicted by evolution|
|Specific examples of genetic function in humans||Failure to predict functional DNA sequences (pseudogenes and chromosomal gene order were mislabeled as “non-functional”)|
In an attempt to move the discussion forward and into the realm of type-1 experiments, creationists have published a testable, predictive model of DNA function from a YEC perspective on one of the few remaining areas of DNA function that has not yet been thoroughly investigated48 (see reference for technical details). If the evolutionists are as confident in their ideas as they claim, then we invite them to publish similar predictions of genetic function, and then to do a head-to-head experiment to test both of the ideas in the laboratory. If evolutionists are unwilling to engage in the experiment that we have proposed, at a minimum, they need to propose a different type-1 experiment.
In short, on the question of human ancestry, evolutionists have a history of making erroneous scientific predictions they have yet to articulate a genuine genetic test by which to eliminate YEC from the discussion and their model does not look promising in light of the trajectory of experimental results in areas where evolution and YEC could theoretically be compared head-to-head.
Chapter 19 - Introduction to Human Genetics
This chapter reviews the basic principles of human genetics to serve as a basis for other studies that deal with specific genetic approaches in clinical research. Genetics is the science that deals with the storage of information within the cell, its transmission from generation to generation, and variation among individuals within a population. Human genetics research has a long history, dating to the study of quantitative traits in the nineteenth century and to the study of Mendelian traits in the first decade of the twentieth century. Medical applications have included such landmarks as newborn screening for inborn errors of metabolism, cytogenetic analysis, molecular diagnosis, and therapeutic interventions such as enzyme replacement. Medical applications historically have been limited to relatively rare disorders caused primarily by mutations in individual genes or structural abnormalities of chromosomes. Recent advances, and especially the sequencing of the human genome, have opened the possibility of understanding genetic contributions to more common disorders, such as diabetes and hypertension. Genetic approaches are now being applied to conditions in virtually all areas of medicine. Genetic information is stored in the cell as molecules of deoxyribonucleic acid (DNA). Each DNA molecule consists of a pair of helical deoxyribose–phosphate backbones connected by hydrogen bonding between nucleotide bases. There are two types of nucleotide bases, purines (adenine [A] and guanine [G]) and pyrimidines (cytosine [C] and thymine [T]).
A Long Time Ago, in a Gamete Far, Far Away.
Life on our planet began with single-cell organisms such as bacteria that reproduce asexually. There isn’t a mother and a father. A cell simply reproduces its genetic material and divides into two or more cells that are genetically identical to the parent cell.
About three or four billion years ago, these single-cell organisms without a distinct nucleus (prokaryotes, or bacteria) began exchanging genetic information in a limited fashion. Then about two billion years ago, organisms such as yeast, with distinct cellular nuclei and specialized structures called organelles (eukaryotes), put their genes in pairs so that they could be divided into two structurally identical gametes (one-cell reproductive units called spores in the case of yeast) and reassembled to create a new organism. This special kind of cell division is called meiosis.
Around 600 million years ago, animals began to evolve specialized gametes — structurally different single-cell units for females (eggs) and males (sperm). Sperm cells fertilize an egg, which then combines the genes of both parents. But such animals, including modern-day turtles, had no specialized sex chromosomes that determine the sex of the offspring. Males and females were genetically identical, and the sex was determined by the temperature at which the egg is incubated.
And finally, starting about 300 million years ago, our ancestors began to evolve sex chromosomes.
In humans, there are 23 pairs of chromosomes, which are structures found within the nucleus of every cell containing the tightly packed molecules known as deoxyribonucleic acid (DNA), the material that carries the genetic code.
One pair of the 23 chromosomes, known as sex chromosomes, determines at conception whether a fertilized egg will develop into a male or female. Today, human females have one pair of identical X chromosomes. Human males, instead of a matched pair, have one X and one smaller Y chromosome.
A human egg contains only an X chromosome. A human sperm contains either an X or a Y chromosome, thereby determining the sex of the offspring after fertilization. XX = female. XY = male.
Dr. Page and his colleagues have spent the better part of the last two decades reconstructing the evolutionary origins of the human X and Y chromosomes. They have traced the origins of these sex chromosomes to ordinary chromosomes called autosomes in evolutionary ancestors that humans share with birds.
“We have been distracted and deceived for the last 50 years by the existence of our sex chromosomes,” Page said. “Most genes that are actually involved in making the different anatomies of human males and females are not on the sex chromosomes. Most of them are on the autosomes. They are exactly the same in males and females. It’s just that the autosomes are read differently in males and females because of the sex chromosomes, just as the entirety of the genome is read differently in males and females.”
In our 23 chromosome pairs, do the 2 members of the pair have distinct or virtually identical sequences? - Biology
Cell Division (Mitosis) In Eukaryotic Cells
- I. Interphase : Period of cell cycle when cell is not dividing. (15 hours)
- A. G1 Phase: Cellular organelles begin to duplicate.
B. S-Phase: DNA replication (chomosomes become doubled).
II. M-Phase (Period of Cell Division): (2 hours)
- A. Karyokinesis (Mitosis or Nuclear Division):
This includes Prophase , Metaphase , Anaphase & Telophase .
2. Homologous Chromosomes: Paternal and Maternal
|Single chromosomes and doubled chromosomes (chromosome doublets). Beginning with prophase, the chromosomes appear as doublets. The clear pink doublets represent a set of maternal doubled chromosomes originally from the mother's egg. The striped blue doublets represent a set of paternal doubled chromosomes originally from the father's sperm. Diploid (2n) organisms such as humans have two sets of chromosomes, one haploid (n) set from the father and one haploid (n) set from the mother. Fertilization of the two haploid sex cells (egg and sperm) results in a diploid zygote (n + n = 2n). Homologous pairs of doublets are represented by one large pink and one large blue doubled chromosome of matching size, and one small pink and one small blue doublet of matching size. In this diagram there are two pairs of homologous chromosome doublets. In a human cell during prophase there are 23 pairs of homologous chromosome doublets, a total of 46 doublets and 92 chromatids. After the chromatids separate during anaphase and the cell divides during telophase, the resulting daughter cells have 23 pairs of single chromosomes, a total of 46. The single chromosomes become doubled again during the S-phase of interphase, prior to the onset of prophase.|
|In this diagram the cell contains 3 pairs of homologous single chromosomes, a total of 6 chromosomes. Since the cell contains a total of 6 chromosomes, it has a chromosome number of 6. Chromosomes A & a represent one pair, B & b represent a second pair, and C & c represent a third pair. Each pair is called a homologous pair because they are matching in size and shape. One member of each pair comes from the mother (pink chromosome) and one member of each pair comes from the father (blue chromosome). Three pink chromosomes in this cell (A, B & C) represent one haploid set of maternal chromosomes from the mother. Three blue chromosomes (a, b & c) in this cell represent one haploid set of paternal chromosomes from the father. Since there are 2 sets of chromosomes in this diagram, the cell is diploid (2n).|
|One chromatid of this eukaryotic chromosome doublet is unravelled, showing a twisted DNA molecule wrapped around beads of histone protein. Each protein bead contains about 200 base pairs on its surface, while the strand between consists of about 50 base pairs. Each protein bead with DNA on its surface is called a nucleosome. Each chromatid is essentially composed of a greatly coiled DNA molecule and protein. The chromatids (DNA molecules) are attached in a region known as the centromere. In these greatly oversimplified illustrations, the centromere is shown as a black dot. It simply represents an area where the sister DNA molecules (chromatids) are attached.|
3. The M-Phase (Cell Division Phase)
|1. Interphase: The cell is not dividing at this time period. The nucleus is composed of dark staining material called chromatin, a term that applies to all of the chromosomes collectively. At this stage the chromosomes are tenuous (threadlike) and are not visible as distinct bodies. A nucleolus is clearly visible inside the nucleus. This body is composed of ribosomal RNA and is the site of protein synthesis within the cell. Prior to cell division, two pairs of protein bodies called centrioles are present in the cytoplasm at one end of the cell. Centrioles are not typically present in plant cells.|
|2. Prophase: One of the centrioles moves to the opposite end of the cell. The opposite ends of the cell are called poles, like the poles of the earth. Each centriole now consists of a pair of protein bodies surrounded by radiating strands of protein called the aster. Plant cells typically do not have the aster or centrioles. Also the nuclear membrane disintegrates and the chromosomes shorten and thicken so that they are visible as distinct rod-shaped bodies. At this time each chromosome is doubled and consists of two chromatids. Each chromatid is essentially composed of a greatly coiled DNA molecule and protein. The chromatids (DNA molecules) are attached in a region known as the centromere. In these greatly oversimplified illustrations, the centromere is shown as a black dot.|
|3. Metaphase: The chromosome doublets become arranged in the central region of the cell known as the equator. They do not necessarily line up single file as the drawing shows. Protein threads called the spindle connect the centromere region of each chromosome doublet with the centrioles at the poles of the cells.|
|4. Anaphase: The chromatids separate from each other at the centromere region and the single chromosomes move to opposite ends (poles) of the cell. When the chromatids separate from each other they are no longer called chromatids. They are now referred to as single chromosomes. The single chromosomes are actually being pulled to opposite ends of the cell as the spindle fibers shorten.|
The corms of autumn crocus ( Colchicum autumnale ), a member of the lily family (Liliaceae), contain the alkaloid colchicine, a spindle poison causing depolymerization of mitotic spindles into tubulin subunits. This essentially dissolves the spindle and stops the cell from completing its mitotic division. Because colchicine can stop plant cells from dividing after the chromatids have separated during anaphase of mitosis, it is a powerful inducer of polyploidy. Seeds and meristematic buds can be treated with colchicine, and the cells inside become polyploid with multiple sets of chromosomes (more than the diploid number). Polyploidy in plants has some tremendous commercial applications because odd polyploids (such as 3n triploids) are sterile and seedless. Polyploid plants (such as 4n tetraploids) typically produce larger flowers and fruits. In fact, many of the fruits and vegetables sold at supermarkets are polyploid varieties. Colchicine has another medical use for people because it reduces the inflammation and pain of gout. It is also used in cancer chemotherapy to stop tumor cells from dividing, thus causing remission of the cancer.
Two additional alkaloids (vinblastine and vincristine) from the Madagascar periwinkle ( Catharanthus roseus ) are also potent spindle poisons. These alkaloids have proven to be very effective in chemotherapy treatments for leukemia and Hodgkin's disease (lymph node and spleen cancer). Like colchicine, they cause the dissolution (depolymerization) of protein microtubules which make up the mitotic spindle in dividing cells. This effectively stops the tumor cells from dividing, thus causing remission of the cancer. Before periwinkle alkaloids were used as a treatment there was virtually no hope for patients with Hodgkin's disease. Now there is a 90 percent chance of survival. This is a compelling reason for preserving the diverse flora and fauna in natural ecosystems. Who knows what cures for dreaded diseases are waiting to be discovered in tropical rain forests or other natural habitats.
|5. Telophase: The chromosomes at each end of the cell begin to organize into separate nuclei, each surrounded by a nuclear membrane. A cleavage furrow or constriction forms in the center of the cell, gradually getting deeper and deeper until the cell is divided into two separate cells. This cytoplasmic division is referred to as cytokinesis. Cytoplasmic division (cytokinesis) in a plant cell is accomplished by a partition or cell plate rather than a cleavage furrow. The following illustration shows cell plate formation in an onion root tip cell:|
|6. Interphase: Now we are back to interphase again, but now there are two daughter cells. Each daughter cell is chromosomally identical with the original (mother) cell. They each have a nucleus that contains a nucleolus and chromatin. The centrioles have divided into four protein bodies and the aster has disappeared. During this phase the chromosomes will replicate and become distinct chromosome doublets as each daughter cell enters prophase.|
|The five major phases of plant mitosis. Unlike animals cells, plant cells do not have centrioles or asters. During telophase, a partition or cell plate divides the cytoplasm rather than a cleavage furrow.|
5. Mitosis & Embryonic Stem Cells
6. Tumors: Uncontrolled Cell Division
When cells divide abnormally they often develop into tissue masses called tumors. Tumors can be produced throughout the body and they can be malignant or benign. Malignant tumors are often referred to as cancers. Some human cancers are caused by viruses, such as certain forms of the herpes virus that causes cervical cancer. Most cancers are neoplastic tumors caused by mutations in the DNA of cells. These mutations interfere with the cell's ability to regulate and limit cell division. Dormant cells enter the M-phase of the cell cycle and begin to divide out of control. Mutations that activate cancer-causing oncogenes or repress tumor-suppressor genes can eventually lead to tumors. Cells have mechanisms that repair mistakes in their DNA however, mutations that affect repair enzymes may cause tumors to form. One of the best examples of the latter mechanism is a basal cell carcinoma.
Excessive exposure to UV radiation from the sun can cause mutations in undifferentiated basal keratinocytes (basal cells) of the epidermis. The specific mutation is called a thymine dimer within the DNA molecule. In normal DNA, the pyrimidine base thymine only pairs with the purine base adenine. When two adjacent thymine bases bond together this causes an abnormal configuration or "kink" in the DNA. Healthy cells can recognize and repair this mistake by excision repair enzymes. In some animals the mutation is repaired by DNA photolyase enzymes that clip out (cleave) the dimer. People with a genetic propensity for skin cancers may have insufficient repair enzymes due to mutations that repress the genes for these repair mechanisms. Although malignant basal cell carninomas generally do not metastasize, they may slowly invade deep layers of the skin and adjacent tissue and eventually be quite destructive. The following image shows the invasive growth of a basal cell carcinoma (technically a morpheaform bcc) that required the removal of about 1/3 of the author's nose. Unlike the nodule growth form of some basal cell carcinomas, the morpheaform bcc proliferates into deeper tissue with aggressive, tentacle-like branches. In addition to an increased number and density of dark-staining basal cells, the latter type of skin cancer produces a proliferation of fibroblasts within the dermis and an increased collagen deposition (sclerosis) that resembles a scar. The tumor appears as a whitish, waxy, sclerotic plaque that rarely ulcerates. It does not form noticeable scabs as in other skin cancers. On the surface of the author's ala (side of nose), this carcimoma resembled a small, concave scar however, it had grown extensively into surrounding tissue. Although the sun is the vital energy source for all life on earth, it can also be a potent carcinogen.
On a positive note for sun exposure, synthesis of vitamin D, a vitamin essential to human biological function, begins with activation of a precursor molecule in the skin by UV rays. Enzymes in the liver and kidneys then modify the activated precursor and finally produce calcitrol, the most active form of vitamin D. During most of the year, a few hours per week of sun exposure to the face and arms is sufficient to meet the body's requirement for the activated calcitrol precursor. In general, fair-skinned people live in northern latitudes with lower light intensity compared with dark-skinned people of the tropical latitudes. Dark skinned people produce greater concentrations of melanin which protects their skin from harmful rays of the sun. Basal cell carcinomas are rare in Blacks and Asians, compared with fair-skinned Whites. It has been suggested that fair-skinned people of northern latitudes might have a slight advantage in synthesizing vitamin D, especially during months of the year in regions with reduced light intensity.
Dividing human cells can be photographed during prophase and metaphase, and all the 46 chromosome doublets can be arranged into 23 homologous pairs. A photographic or digital printed image called a karyotype is then made showing all the chromosomes neatly lined up in homologous pairs, from 1 through 23. Karotypes are very useful in determining chromosomal abnormalities, such as chromosomal deletions (missing genes) or incorrect numbers. For example, a person with Down's syndrome would have three number 21 chromosomes rather than two.
Karyotypes can also reveal the gender of a person. In addition to the 22 pairs of chromosomes (autosomes) in human somatic (body) cells, females have a 23rd pair consisting of two X chromosomes. The 23rd pair of males consists of an X and a Y chromosome. The smaller Y chromosome contains a region of DNA on the short arm of the Y responsible for masculinization of the fetus. In females one of the two X chromosomes appears as a condensed, dark-staining Barr body inside the nucleus of somatic cells, near the nuclear membrane. This structure is named after its discoverer, Murray Barr. Since Barr bodies only appear in nuclei with more than one X chromosome, they are not present in male cells. Up until the early 1990s, the lack of Barr bodies in nuclei from cheek epithelial cells of women could disqualify them for competition in the Olympic Games.
The calico cat is a sexual mosaic characterized by blotches of black, yellow and white fur. The genes (alleles) for black and yellow are linked to the same loci on two different X chromosomes. This is why calico cats are typically female because they have two X chromosomes, one with the black gene and one with the yellow gene. Since the black gene is dominant over yellow, how does the mosaic color pattern develop? The Barr body concept provides a nice cellular explanation for the patches of black and yellow fur. In regions with black fur, the black gene is active and the yellow gene is located on an inactive Barr body. In regions with yellow fur, the black gene is on the inactive Barr body while the yellow gene is on the active X chromosome. At an early stage in the cat's embryonic development, certain X chromosomes become inactive Barr bodies, apparantly at random. In the descendants of these cells, the same chromosomes are inactive, leaving the cells with only one functional allele for coat color. A rare calico male probably has an XXY karotype resulting in maleness, black fur and yellow fur. By the way, the white patches result from a gene interaction involving the "spotting gene," which blocks melanin synthesis entirely.
Gender verification in the Olympic Games now employs sophisticated DNA testing rather than counting Barr bodies within the nuclei of cells. The test is designed to detect the presence of the SRY gene (sex region Y chromosome), a region of DNA on the short arm of the Y chromosome responsible for masculinization of the fetus. Cells from the buccal mucosa (squamous epithelial cells), often called "cheek cells" in general biology classes, are obtained by gently scraping the inside of the mouth with a toothpick. The DNA in the nuclei of these cells is amplified using the PCR technique (polymerase chain reaction). If present, the SRY gene will show up as a unique banding pattern by electrophoresis on agar gels.
The following table shows different possible combinations of X and Y chromosomes in people. The gender of some of these chromosomal karyotypes and syndromes cannot be correctly identified using the Barr body technique:
The common potato (Solanum tuberosum) is an example of a tetraploid organism, carrying four sets of chromosomes. During sexual reproduction, each potato plant inherits two sets of 12 chromosomes from the pollen parent, and two sets of 12 chromosomes from the ovule parent. The four sets combined provide a full complement of 48 chromosomes. The haploid number (half of 48) is 24. The monoploid number equals the total chromosome number divided by the ploidy level of the somatic cells: 48 chromosomes in total divided by a ploidy level of 4 equals a monoploid number of 12. Hence, the monoploid number (12) and haploid number (24) are distinct in this example.
However, commercial potato crops (as well as many other crop plants) are commonly propagated vegetatively (by asexual reproduction through mitosis),  in which case new individuals are produced from a single parent, without the involvement of gametes and fertilization, and all the offspring are genetically identical to each other and to the parent, including in chromosome number. The parents of these vegetative clones may still be capable of producing haploid gametes in preparation for sexual reproduction, but these gametes are not used to create the vegetative offspring by this route.
Some eukaryotic genome-scale or genome size databases and other sources which may list the ploidy levels of many organisms: