Any experts on evolution here?

Discussion in 'Biology & Genetics' started by Io Aurelia, Mar 10, 2002.

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  1. scilosopher

    scilosopher Registered Senior Member

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    Eflex,
    Current estimates are only going to be order of magnitude. For most genes with no homology, they get the estimate by using genscan a gene prediction program. It joins and splits genes a lot (not because it is poorly written/designed, but due to inherent practical constraints). Anyhow, I was just pointing out that even a conservative estimate of the number of possible combinations is MUCH larger than the population and not well explored.

    But you're right - as large as it is it could be much larger. Combine that with environmental differences and things like training we have explored only an itty bitty fraction of the potential of humanity. I don't know personally if I find that reassuring or scary.
     
    scilosopher, Apr 2, 2002
    #21

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  3. paulsamuel

    paulsamuel Registered Senior Member

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    reply to scilosopher

    I think it's a matter of perspective. If one looks at an individual, it may not appear that mating is random. But when observing an entire population, mating is fairly random. Non-random processes do exist however, for example sexual selection. The effects of these non-random processes on evolution have been extensively studied.

    The criterion for random mating in a population is that an individual has an equal chance of mating with another individual (of the opposite sex). This is clearly the ideal and that, in reality, humans don't mate in a purely random fashion. However, it is close to random (I'm looking for some refs. that have shown this). There have been attempts to reveal mechanisms for sexual selection in humans, but none have been satisfactory, AFAIK.

    I'm glad you brought up that point concerning abilities. This is exactly what I was thinking of. For example, abilities that we have now (observation based prediction of behavior and motivation); one can envision that individuals could have a refinement of these abilities (either through selection or training) giving them an appearance of mind-reading. If the refined abilities are heritable, then they would be subject to selection, and, if selection was strong enough, they could sweep through a population. OTOH, abilities that we do not currently posess would have to arise de novo.

    You're right when you point out that I'm wrong when I imply that unconscious abilities would not be subject to selection. I was thinking specifically about mind-reading. If an individual has an ability, like mind-reading, but that ability is not used, then that ability would not be subject to selection, and the ability would be lost due to drift (think of mole's eyes). That is a more accurate statement about what I was trying to say.
     
    paulsamuel, Apr 2, 2002
    #22

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  5. kmguru

    kmguru Staff Member

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    Has anybody tried to create a pig with the smallest set of genes and what was the result? Can a human actually survive with 40,000 genes?
     
    kmguru, Apr 2, 2002
    #23

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  7. Eflex tha Vybe Scientist

    Eflex tha Vybe Scientist Registered Senior Member

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    Good question

    I dont believe in the concept of "junk DNA"
     
    Eflex tha Vybe Scientist, Apr 2, 2002
    #24
  8. paulsamuel

    paulsamuel Registered Senior Member

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    reply to kmguru and EFlex

    According to a recent article in the Balt. Sun (Feb., 23: pg. 1A), data from the Human Genome Project indicate humans have about 35000 genes. However, "the number of proteins is expected to be more vast - the best scientific guesses put the count in the hundreds of thousands." So, obviously we can live with not just 40000 genes, but with only 35000 genes.

    Eflex, "junk DNA" is not a concept, it's a fact of nature, independent of anyone's beliefs.
     
    paulsamuel, Apr 2, 2002
    #25
  9. scilosopher

    scilosopher Registered Senior Member

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    Paul,
    My personal perspective is that most things that appear random just have a bunch of factors where you lack the information to generate a model. Therefore you can't get a good correlation between your data in the absence of that info. Especially when examination at another scale seems to indicate otherwise. The more complicated the mechanisms, the more data you can amass and still not fit it well. I certainly know my interactions with the opposite sex are complicated (often unnecessarily). They might seem pretty random to someone who doesn't know what I'm thinking, but there is a method to my madness.

    Regarding the generation of esp, most evolution seems to come from coopting genes to a new function. Maybe certain brain regions can act a bit like an antenna even though they didn't arise for that function. If that weak signal in the background of other senses that give information to the brain can be used to create a more coherent picture ...

    On the whole junk DNA thing, there are two observations about higher organisms and their use of DNA that make one wonder if it really is junk 1) DNA serves a structural role in chromosomes - both playing a role in positioning functional elements in chromatin and serving as scaffolding for physical manipulation; 2) The amount of regulatory to coding DNA shows a large increase (though there are ploidy effects - ie gene duplication can moderate this effect).

    enjoyable conversation ...
     
    scilosopher, Apr 3, 2002
    #26
  10. Eflex tha Vybe Scientist

    Eflex tha Vybe Scientist Registered Senior Member

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    Re: reply to kmguru and EFlex

    I'm not we fully understand DNA to be avle to classify any of it as junk.

    Repetition and redundancy is a good possibility for some parts of our DNA.
    (A back up copy of critical sequences)

    Nature is known for its efficiency and "junk DNA" is a really inefficient concept.
     
    Eflex tha Vybe Scientist, Apr 3, 2002
    #27
  11. paulsamuel

    paulsamuel Registered Senior Member

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    reply to scilosopher

    You say "most evolution seems to come from coopting genes to a new function." This is definately true in some cases, but it is certainly not true for most evolution. But, I get your point, and it's a good one, but in the case of ESP or mind reading, there's unlikely to be the raw material in our genes for co-opting to occur.

    Concerning junk DNA, I am not saying that all non-coding DNA is junk. I am saying that of the non-coding DNA, some is junk. There's lots of evidence for this. Look at pseudogenes, transposons, microsatellites. Look at the genome of some amphibians where they have genomes hundreds of times the size of humans.
     
    paulsamuel, Apr 3, 2002
    #28
  12. paulsamuel

    paulsamuel Registered Senior Member

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    882
    reply to Eflex

    We do understand enough about DNA to be able to explain the source of some non-coding DNA (i.e. mistakes in replication, duplication, genetic drift and the creation of pseudogenes, birth and death of microsatellites, etc.). When this kind of stuff happens, it (the new non-functional DNA) can just hang around. This is the junk. It happens, it's identifiable and it's observable. No big deal. There's nothing "holy" about DNA, where it all has to be functional.

    The efficiency of Nature is a misconception shared by many non-biologists. In fact, Nature is inefficient, and there are numerous examples of it. I suggest reading Stephen J. Gould. He loves to point out the inefficiency of Nature as support for evolution.

    There is actually no "back-up" DNA. Genes are functional or not. If not functional, they're subject to drift (accumulation of mutation), therefore they cannot back-up anything.
     
    paulsamuel, Apr 3, 2002
    #29
  13. scilosopher

    scilosopher Registered Senior Member

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    435
    Paul,
    Agreed. I meant most new function seems to be due to duplication as the genes present already do something else useful. I've also always wondered if domain structures can also come up from new domains being selected out of the flanking sequence and being tested in moderation by occasional readthrough on stops and such.

    Regarding junk, just because something appears by accident or even blatant mistake doesn't mean that it doesn't end up having a functional effect. Usually the function is bad. Occassionally it's good. Having junk lying to around to be selected on (like useless extra copies of a gene) is necessary or changes are going to be contrained from the fact that it is contrained to always effect existing function. Separating natures inefficiency to clear that from its retention of allowing such mistakes because they are beneficial is not a level of resolution I believe we have.

    I agree that most is junk right now, but one man's junk can become another man's treasure.
     
    scilosopher, Apr 3, 2002
    #30
  14. paulsamuel

    paulsamuel Registered Senior Member

    Messages:
    882
    reply to scilosopher

    It really doesn't seem likely to me that junk DNA has any future potential. Are you aware of the Mueller's ratchet concept? I am not aware of any evidence that junk DNA has ever become anything useful (or even anything bad). I would happily read anything you have to pass along. Thanks
     
    paulsamuel, Apr 3, 2002
    #31
  15. kmguru

    kmguru Staff Member

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    11,757
    I am not a DNA expert so I am confused a little bit about the 35,000 number. What it is exactly? Here is the basics as I understand it.

    The Basics
    Cells are the fundamental working units of every living system. All the instructions needed to direct their activities are contained within the chemical DNA (deoxyribonucleic acid).

    DNA from all organisms is made up of the same chemical and physical components. The DNA sequence is the particular side-by-side arrangement of bases along the DNA strand (e.g., ATTCCGGA). This order spells out the exact instructions required to create a particular organism with its own unique traits.

    The genome is an organism’s complete set of DNA. Genomes vary widely in size: the smallest known genome for a free-living organism (a bacterium) contains about 600,000 DNA base pairs, while human and mouse genomes have some 3 billion. Except for mature red blood cells, all human cells contain a complete genome.

    DNA in the human genome is arranged into 24 distinct chromosomes--physically separate molecules that range in length from about 50 million to 250 million base pairs. A few types of major chromosomal abnormalities, including missing or extra copies or gross breaks and rejoinings (translocations), can be detected by microscopic examination. Most changes in DNA, however, are more subtle and require a closer analysis of the DNA molecule to find perhaps single-base differences.

    Each chromosome contains many genes, the basic physical and functional units of heredity. Genes are specific sequences of bases that encode instructions on how to make proteins. Genes comprise only about 2% of the human genome; the remainder consists of noncoding regions, whose functions may include providing chromosomal structural integrity and regulating where, when, and in what quantity proteins are made. The human genome is estimated to contain 30,000 to 40,000 genes.

    Although genes get a lot of attention, it’s the proteins that perform most life functions and even make up the majority of cellular structures. Proteins are large, complex molecules made up of smaller subunits called amino acids. Chemical properties that distinguish the 20 different amino acids cause the protein chains to fold up into specific three-dimensional structures that define their particular functions in the cell.

    The constellation of all proteins in a cell is called its proteome. Unlike the relatively unchanging genome, the dynamic proteome changes from minute to minute in response to tens of thousands of intra- and extracellular environmental signals. A protein’s chemistry and behavior are specified by the gene sequence and by the number and identities of other proteins made in the same cell at the same time and with which it associates and reacts. Studies to explore protein structure and activities, known as proteomics, will be the focus of much research for decades to come and will help elucidate the molecular basis of health and disease.

    So it occurs to me that we have to understand the whole DNA base pairs to create a life form. Is that correct? And knowing just 35,000 genes itself is not enough anymore than having a jet engine without the wings , tail or body to fly? Did I miss something here?

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    Some other stuff:

    By the Numbers

    The human genome contains 3164.7 million chemical nucleotide bases (A, C, T, and G).
    The average gene consists of 3000 bases, but sizes vary greatly, with the largest known human gene being dystrophin at 2.4 million bases.
    The total number of genes is estimated at 30,000 to 40,000, much lower than previous estimates of 80,000 to 140,000 that had been based on extrapolations from gene-rich areas as opposed to a composite of gene-rich and gene-poor areas.
    The order of almost all (99.9%) nucleotide bases is exactly the same in all people.
    The functions are unknown for more than 50% of discovered genes.
    The Wheat from the Chaff
    About 2% of the genome encodes instructions for the synthesis of proteins.
    Repeated sequences that do not code for proteins (junk DNA) make up at least 50% of the human genome.
    Repetitive sequences are thought to have no direct functions, but they shed light on chromosome structure and dynamics. Over time, these repeats reshape the genome by rearranging it, thereby creating entirely new genes or modifying and reshuffling existing genes.
    During the past 50 million years, a dramatic decrease seems to have occurred in the rate of accumulation of these repeats.
    How It's Arranged
    The human genome’s gene-dense “urban centers” are composed predominantly of the DNA building blocks G and C.
    In contrast, the gene-poor “deserts” are rich in the DNA building blocks A and T. GC- and AT-rich regions usually can be seen through a microscope as light and dark bands on the chromosomes.
    Genes appear to be concentrated in random areas along the genome, with vast expanses of noncoding DNA between.
    Stretches of up to 30,000 C and G bases repeating over and over often occur adjacent to gene-rich areas, forming a barrier between the genes and the “junk DNA.” These CpG islands are believed to help regulate gene activity.
    Chromosome 1 has the most genes (2968), and the Y chromosome has the fewest (231).
    How the Human Genome Compares with Those of Other Organisms
    Unlike the human’s seemingly random distribution of gene-rich areas, many other organisms’ genomes are more uniform, with genes evenly spaced throughout.
    Humans have on average three times as many kinds of proteins as the fly or worm because of mRNA transcript “alternative splicing” and chemical modifications to the proteins. This process can yield different protein products from the same gene.
    Humans share most of the same protein families with worms, flies, and plants, but the number of gene family members has expanded in humans, especially in proteins involved in development and immunity.
    The human genome has a much greater portion (50%) of repeat sequences than the mustard weed (11%), the worm (7%), and the fly (3%).
    Although humans appear to have stopped accumulating repetitive DNA over 50 million years ago, there seems to be no such decline in rodents. This may account for some of the fundamental differences between hominids and rodents, although estimates of gene numbers are similar in both species. Scientists have proposed many theories to explain evolutionary contrasts between humans and other organisms, including life span, litter sizes, inbreeding, and genetic drift.
    Variations and Mutations
    Scientists have identified about 1.4 million locations where single-base DNA differences (SNPs, see Goals Box: Sequence Variation) occur in humans. This information promises to revolutionize the processes of finding chromosomal locations for disease-associated sequences and tracing human history.
    The ratio of germline (sperm or egg cell) mutations is 2:1 in males vs females. Researchers point to several reasons for the higher mutation rate in the male germline, including the greater number of cell divisions required for sperm formation than for eggs.
    Applications, Future Challenges
    Deriving meaningful knowledge from the DNA sequence will define research through the coming decades to inform our understanding of biological systems. This enormous task will require the expertise and creativity of tens of thousands of scientists from varied disciplines in both the public and private sectors worldwide.
    The draft sequence already is having an impact on finding genes associated with disease. Genes have been pinpointed and associated with numerous diseases and disorders including breast cancer, muscle disease, deafness, and blindness. Additionally, finding the DNA sequences underlying such common diseases as cardiovascular disease, diabetes, arthritis, and cancers is being aided by the human SNP maps generated in the HGP in cooperation with the private sector. These genes and SNPs provide focused targets for the development of effective new therapies.

    One of the greatest impacts of having the sequence may well be in enabling an entirely new approach to biological research. In the past, researchers studied one or a few genes at a time. With whole-genome sequences and new automated, high-throughput technologies, they can approach questions systematically and on a grand scale. They can study all the genes in a genome, for example, or all the gene products in a particular tissue or organ or tumor, or how tens of thousands of genes and proteins work together in interconnected networks to orchestrate the chemistry of life.
     
    kmguru, Apr 3, 2002
    #32
  16. Eflex tha Vybe Scientist

    Eflex tha Vybe Scientist Registered Senior Member

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    Re: reply to Eflex

    Well

    I've studied a little biology in my day...
    I'm more of a Biochemist that found his way into Computer Science

    1. Nature is capable of becoming more efficient.

    2. There are prime examples of the efficeincy of Nature
    Water - the H20 molecule is a pretty efficient solute
    Hydrogen Bonding
    The creation of Hexagonal Bee Honey Combs
    The spiral formation of Spiders Webs

    3. As electro chemical machines, we humans are pretty efficient at dopamine reuptake at the synaptic level.
     
    Eflex tha Vybe Scientist, Apr 3, 2002
    #33
  17. scilosopher

    scilosopher Registered Senior Member

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    435
    Paul,
    I don't know Mueller's ratchet, though it sounds vaguely entropic ...

    In terms of evidence for pure junk DNA doing stuff, I don't know. The size of regulatory regions seems to suggest there is need for more filler DNA to keep promoter modules from interacting. The usefulness of duplications is seen in the amount in evidence in evolution.

    Kmguru,
    I'm not sure what you meant exactly, but the number is relavent to estimates of potential complexity in the gene pool as well as the organism itself. Clearly more is necessary for a complete understanding of a person.
     
    scilosopher, Apr 3, 2002
    #34
  18. Eflex tha Vybe Scientist

    Eflex tha Vybe Scientist Registered Senior Member

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    190
    Re: reply to scilosopher

    scientists now generally believe that "junk" DNA must contain some kind of coded information. But the code and its function is yet completely unknown

    http://www.psrast.org/junkdna.htm

    I find it hard to believe that more than half of our genetic code is Useless

    Isn't there a possibility that we dont truly understand the complete function of DNA ?

    therefore we are calling pieces of our genetic code "junk" when its actually pretty important?
     
    Eflex tha Vybe Scientist, Apr 3, 2002
    #35
  19. paulsamuel

    paulsamuel Registered Senior Member

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    882
    reply to kmguru

    Wow, what a post!

    some notes:

    you wrote: "Except for mature red blood cells, all human cells contain a complete genome."
    Gametes are haploid, so sperm and eggs can be considered to have an incomplete genome.

    you wrote: "DNA in the human genome is arranged into 24 distinct chromosomes"
    Actually, although there are 24 distinct human chromosomes, each human cell (except red blood cells and gametes) contains 23 chromosomal pairs (46 chromosomes in all).

    you wrote: "So it occurs to me that we have to understand the whole DNA base pairs to create a life form."
    We'll need much more than that, but I don't think creating a life form is the goal of science.

    you wrote: "The order of almost all (99.9%) nucleotide bases is exactly the same in all people."
    I would love to know where you got this factoid. Would you please pass along a ref. for this? Thanks.

    you wrote: "During the past 50 million years, a dramatic decrease seems to have occurred in the rate of accumulation of these repeats."
    Again, will you please pass along a ref. for this?

    Did you just copy and paste the bottom part of this post? If you did, can you supply an URL? Thanks
     
    paulsamuel, Apr 3, 2002
    #36
  20. Eflex tha Vybe Scientist

    Eflex tha Vybe Scientist Registered Senior Member

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    190
    Re: reply to Eflex

    ummmmm
    maybe "back up" was the wrong word.

    Remember, I've been workin' in the Computer Science industry for over 5 years now...

    Evolutionarily speaking...

    Isnt the whole point of DNA is to have a pristine copy of genetic material avialable for replication.

    weren't the first single celled organisms RNA only?

    and havent we evolved to store our genetic code as DNA in the nucleus to minimize the damage done by environmental factors such as UV rays, and other forms of radiation?
     
    Eflex tha Vybe Scientist, Apr 3, 2002
    #37
  21. kmguru

    kmguru Staff Member

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    11,757
    kmguru, Apr 3, 2002
    #38
  22. paulsamuel

    paulsamuel Registered Senior Member

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    882
    reply to Eflex

    I don't really want to get into trading examples of efficiency (or lack thereof).

    But some comments on your examples:

    H2O; really only one way to make it, not a good example of efficiency.

    honeycomb; this is a good example of maximizing space, but studies have shown that a circle would be better and that bees use hexagons to come as close to a circle as they can. There are published references on this topic.

    The point I was trying to make is that Nature is constrained by the raw material with which it works and that many "solutions" could be considered jury-rigged.

    In regards to junk DNA, as I stated earlier, I am not saying that all non-coding DNA is junk, but junk DNA exists (I give examples in a previous post). I take this quote from the web-page you supplied, "The Science article reports on a paper suggesting that the non-coding 97% of the DNA, commonly referred to as junk DNA, might have a function." I believe the 97% is an overestimation, but even if it's not, that leaves 3% junk.

    you say, "scientists now generally believe that "junk" DNA must contain some kind of coded information."
    I don't believe this. Could you supply a reference? No scientist could mistake coding DNA for junk. But, I agree that not all non-coding DNA is junk. I don't know of any who would say our genetic code is junk. Our genetic code is identifiable by what are called ORF's (open reading frames) which are DNA sequences consisting of triplets (three nucleotides in a row that "code" for an amino acid). Not all of our DNA is coding, this is a well known fact.


    In regards to "back-up DNA": during DNA replication, mistakes occur. There are however enzymes that can fix mistakes in replication (and transcription for that matter) but successful repair is not 100%.
    The theory is that the first live organisms were RNA based.
    It is not universally accepted that the nucleus is membrane bound for protection from the environment, it could be just a mechanism for compartmentilization. A good ref. for why there are membrane bound stuff in eukaryotic cells: Lynn Margulis, and her theories of endosymbiosis.
     
    paulsamuel, Apr 3, 2002
    #39
  23. paulsamuel

    paulsamuel Registered Senior Member

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    882
    reply to scilosopher

    Muller's ratchet is a hypothesis of irreversible accumulation of deleterious mutations (the analogy being that the ratchet is unidirectional). So, a mutation occurring at a locus would be highly unlikely to fix itself (go back to the original state). When including multiple mutations at multiple loci, it's impossible.

    I guess it's analogous to entropy in a way.

    Well, I'd like to see some evidence of junk DNA somehow obtaining some functionality, but I don't believe it happens.

    Since we know some methods or origins of junk DNA, I think it just accumulates. Is there some mechanism of excising non-functional DNA? If there is what happens to the DNA that is excised? I don't think there are mechanisms for this.
     
    paulsamuel, Apr 3, 2002
    #40
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