Evolution Must Happen, it is logical

We have spent considerable time discussing various forms of evidence for evolution. Plus a lot of discussion about mechanisms and looking ofr it taking place currently.I want to suggest that it is possible to start with a very small set of facts about the real world and arrive at evolution HAVING to happen.Facts:
1) Our phenotypes (bodyily physical forms ) are very greatly determined by our genotype( the detailed sequences of our DNA)
2) The genotype changes with each individual born (perhaps not for each bacteria or others but almost all). These changes include sexual (and other) mixing up of the genome to produce a new unique one and a variety of mutations which produce completely novel sequences.
3) Not all individuals born will produce offspring and different individuals will produce different numbers of surviving progeny.
4) The reasons for 3 will vary a great deal. Much of it will be random accident. This will apply to almost all individuals equally (that is the nature of "random"). However, some portion of the differences are a result of genetic differences between individuals.
5) At some point in a populations duration there will be changes in environmental conditions that change the "rules" for who will reproduce more successfully and who will reproduce less successfully.
6) The genetic changes can affect all aspects of the resulting individuals.
7) There are cases where populations will be split or separated by a variety of circumstance (new river, desert, mountain, swamp, lake or what have you)
8) There is a rather continuous range of variation in DNA across ALL species. That is we can make a small (1, 2 3 or so) % change in the DNA of one species and get the DNA of another. From this new one we can find another few % and get to a third. Such changes allow us to connect most (perhaps not all) forms of life with each other.Reasoning:Micro-EvolutionGiven the first 5 above:
Evolution HAS to happen!
If not all individuals reproduce equally successfully and if the environment allows those with some particular characteristics to have a non-random increase in success then the population MUST change it's make up to be different that it was.I think that everyone will agree with this. This is adaptation or "micro-evolution".Macro-EvolutionNow given 6 behaviours that lead to choice of mates or the finding of mates can change or that the nature of the geneome changes can produce individuals that can NOT interbreed Given 7 that allows populations to change INDEPENDANTLY of each other there is nothing to stop the split populations from losing the ability to interbreed. This is the definition of new species. It is also macro-evolution in the biological sense of the word. Many creationists seem to agree that this too is possible although they are rather fuzzy about actually saying so. Some clearly do not agree. For those that don't I would like to see they idea of what stops it.Full Diversity of LifeGiven that we have separated populations that are still undergoing change (and may be split again and again since the mechanisms of 7 keep operating) and given 8 (mostly continuous DNA ) then there is nothing to stop what was one population from diverging into a large number of more and more different populations. The differences will grow large enough to be at the Genus, Family, order and higher levels of taxonomy. There is nothing to stop this and like water will run down hill and follow the low spots and channels life will evolve to fill many different niches producing vary different forms.This is, of course, what creationists (in the common use of the term) disagree with. But why? What do they have to show that there is an error in fact or reasoning.This belongs in biological evolution.

Thread moved here from the Proposed New Topics forum.

I'm not sure how clear this is. It is certainly true that there are many proteins or DNA sequences for conserved genes where the differences could easily be shown to be within that1-3% range. But when you are looking at the whole genome and especially when you look at large scale genomic arrangements it is very hard to quantify it in simple terms of a percentage.Perhaps you should specify what DNA you are specifically looking at variation in, i.e. protein coding sequences or regulatory sequences etc... Or where you are getting your specific values. Is it DNA-DNA hybridisation affinity or comparisons from whole genome shotgunning? How are you weighting things like synteny to affect the percentage?TTFN,WK

Thanks WK, you're comments are exacty what I need.The first answer is I don't know what I'm looking for. Can you help sort out what would make sense? I would think that the right thing to look at here is the number of base pair differences in coding areas.The statement of "fact" that I have made is not based on enough knowledge. There is also the problem that by the time higher taxa are examined there has been time to diverage considerably with the intervening genomes gone now. What I am conjecturing is since we and the mouse share about 60% (of something or another ). There may be enough 2 or 4 % differences in extant animals to bridge the gaps. No?

That is probably the most straightforward thing to do and certainly the simplest, sadly there is a considerable chance that an awful lot of the relevant variation will be in regulatory regions, or even in larger scale chromosomal positioning.This is certainly doable in some instances in terms of small scale systems, but I doubt that you could account for all the differences between anything but species which have just this instant, in evolutionary terms, diverged. I think it is a pretty ambitious conjecture. Even going by an optimistic evaluation based on your numbers you would need to look at at least 10 different species although a higher resolution would be desirable. That is assuming that the 2-4% differences are cumulative, I suspect at least a significant portion of it is likely to be novel for that particular lineage.I'm fairly sceptical that you could do this effectively even with the whole genomes of a dozen or so suitable species. You could certainly construct a much more accurate phylogeny than most that are extant at the moment, and also probably make some well educated guesses as to the genetic makeup of the latest common ancestor but I doubt that there are sufficient extant species of the neccessary lineages to allow for a really full accounting of all the variation between mouse and man for instance. I may be being pessimistic however, I don't really know what the actual numbers for this sort of project would turn out to be.TTFN,WK

Ok, so item 8 isn't factual. Is there another way of getting there?

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Ok, so item 8 isn't factual. Is there another way of getting there?

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Theoretically, the best way to construct phylogenies is to use genetic sequences that are strongly conserved and common to all species under investigation. Ribosomal RNA (rRNA) is one way in which scientists are now investigating the genetic relatedness of divergent species. Do a search for "rRNA phylogenies" and you will get a lot of hits. rRNA (or more accurately SSU rRNA phylogenies) research is still early in development but it does look promising.Here are a few abstracts dealing with rRNA and protein phylogenies. You will notice that rRNA phylogenies are useful for divergent species while other proteins are useful for finer-grade species:This abstract uses rRNA to counteract the occurence of horizontal gene transfer (genetic transfer between different species) in order to construct phylogenies within bacteria and how they relate to eukaryotes.
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Reconstructing evolutionary relationships from functional data: a consistent classification of organisms based on translation inhibition response - PubMed
Mol Phylogenet Evol. 2005 Feb;34(2):371-81. Epub 2004 Dec 15. Related Articles, LinksReconstructing evolutionary relationships from functional data: a consistent classification of organisms based on translation inhibition response.Briones C, Manrubia SC, Lazaro E, Lazcano A, Amils R.Centro de Astrobiologia, Carretera de Ajalvir Km. 4, 28850 Torrejon de Ardoz, Madrid, Spain.The last two decades have witnessed an unsurpassed effort aimed at reconstructing the history of life from the genetic information contained in extant organisms. The availability of many sequenced genomes has allowed the reconstruction of phylogenies from gene families and its comparison with traditional single-gene trees. However, the appearance of major discrepancies between both approaches questions whether horizontal gene transfer (HGT) has played a prominent role in shaping the topology of the Tree of Life. Recent attempts at solving this controversy and reaching a consensus tree combine molecular data with additional phylogenetic markers. Translation is a universal cellular function that involves a meaningful, highly conserved set of genes: both rRNA and r-protein operons have an undisputed phylogenetic value and rarely undergo HGT. Ribosomal function reflects the concerted expression of that genetic network and consequently yields information about the evolutionary paths followed by the organisms. Here we report on tree reconstruction using a measure of the performance of the ribosome: antibiotic sensitivity of protein synthesis. A large database has been used where 33 ribosomal systems belonging to the three major cellular lineages were probed against 38 protein synthesis inhibitors. Different definitions of distance between pairs of organisms have been explored, and the classical algorithm of bootstrap evaluation has been adapted to quantify the reliability of the reconstructions obtained. Our analysis returns a consistent phylogeny, where archaea are systematically affiliated to eukarya, in agreement with recent reconstructions which used information-processing systems. The integration of the information derived from relevant functional markers into current phylogenetic reconstructions might facilitate achieving a consensus Tree of Life.
----------------------------------------------------------------------This abstract demonstrates that other conserved proteins may be more useful in constructing phylogenies of species that are more closely related.
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Molecular phylogeny of the nasuta subgroup of Drosophila based on 12S rRNA, 16S rRNA and CoI mitochondrial genes, RAPD and ISSR polymorphisms - PubMed
Genes Genet Syst. 2004 Oct;79(5):293-9. Related Articles, LinksMolecular phylogeny of the nasuta subgroup of Drosophila based on 12S rRNA, 16S rRNA and CoI mitochondrial genes, RAPD and ISSR polymorphisms.Nagaraju J, Ranganath HA; Nagaraja.Drosophila Stock Centre, Department of Studies in Zoology, University of Mysore.The nasuta subgroup is a cluster of morphologically almost similar forms with a wide range of geographic distribution. During the last three decades nature of inter-relationship among the members has been investigated at different levels of organization. The phylogenetic relationships of the members of the nasuta subgroup of the immigrans species group of Drosophila was made by employing Random Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeats-PCR (ISSR-PCR) polymorphisms, mitochondrial 12S rRNA, 16S rRNA and Cytochrome C Oxidase subunit I (CoI) gene sequences. The phylogenetic tree generated by RAPD analysis is in nearly complete congruence with the classification based on morphophenotypic characters. The 12S and 16S rRNA genes were highly conserved across the nasuta subgroup and revealed only 3 and 4 variable sites respectively, of which only one site was informative. The CoI gene, on the other hand, revealed 57 variable sites of which 25 sites were informative. All the three species of orbital sheen complex were included in a major cluster in the phylogenetic trees derived from mitochondrial gene sequence data consistent with the morphophenotypic classification. The CoI analysis placed two species of frontal sheen complex, D. n. nasuta and D. n. albomicans in two different clades and this is inconsistent with morphological classification. The molecular clock suggested that divergence between the kohkoa complex and the albomicans complex occurred ~2.2 MYA, indicating recent evolution of the nasuta subgroup. The higher transition bias in the mitochondrial genes reported in the present study also suggested recent evolution of the nasuta subgroup.
----------------------------------------------------------------------A great study that uses new methods of comparing rRNA. It shows that the genetic data independently verifies the phylogenies constructed through morphological traits within Insectevora (insects).
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Aligned 18S and insect phylogeny - PubMed
Syst Biol. 2004 Jun;53(3):506-14. Related Articles, LinksAligned 18S and insect phylogeny.Kjer KM.Department of Ecology Evolution and Natural Resources, 14 College Farm Road, Cook College, Rutgers University, New Brunswick, NJ 08901, USA. kjer@aesop.rutgers.eduThe nuclear small subunit rRNA (18S) has played a dominant role in the estimation of relationships among insect orders from molecular data. In previous studies, 18S sequences have been aligned by unadjusted automated approaches (computer alignments that are not manually readjusted), most recently with direct optimization (simultaneous alignment and tree building using a program called "POY"). Parsimony has been the principal optimality criterion. Given the problems associated with the alignment of rRNA, and the recent availability of the doublet model for the analysis of covarying sites using Bayesian MCMC analysis, a different approach is called for in the analysis of these data. In this paper, nucleotide sequence data from the 18S small subunit rRNA gene of insects are aligned manually with reference to secondary structure, and analyzed under Bayesian phylogenetic methods with both GTR+I+G and doublet models in MrBayes. A credible phylogeny of Insecta is recovered that is independent of the morphological data and (unlike many other analyses of 18S in insects) not contradictory to traditional ideas of insect ordinal relationships based on morphology. Hexapoda, including Collembola, are monophyletic. Paraneoptera are the sister taxon to a monophyletic Holometabola but weakly supported. Ephemeroptera are supported as the sister taxon of Neoptera, and this result is interpreted with respect to the evolution of direct sperm transfer and the evolution of flight. Many other relationships are well-supported but several taxa remain problematic, e.g., there is virtually no support for relationships among orthopteroid orders. A website is made available that provides aligned 18S data in formats that include structural symbols and Nexus formats.
----------------------------------------------------------------------This message has been edited by Loudmouth, 01-11-2005 13:46 AM

I will have to look in more detail. That stuff looks interesting.I think it might not be what I am looking for.It may be very useful for determining what happened in actual fact.What I am trying to get to is a logical argument that evolution HAD to happen (or has to happen).I need something to say that there are no really big gaps in spite of how different things look from Man to Mouse to fish to worm to...
Even tough I know that the time from some of the branch points may mean there are rather large genetic gaps between species today I am trying to see if you look at the tip of the branches now you can find nearby ones on the tree of life. And then go from branch tip to branch tip with smallish genetic differences.I'm not sure that your information directly answers that. It does seem to hint that it might.It will in intesting (very) over the next decade as we start to crank out more and more genomes.This message has been edited by NosyNed, 01-11-2005 16:34 AM

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I need something to say that there are no really big gaps in spite of how different things look from Man to Mouse to fish to worm to...
Even tough I know that the time from some of the branch points may mean there are rather large genetic gaps between species today I am trying to see if you look at the tip of the branches now you can find nearby ones on the tree of life. And then go from branch tip to branch tip with smallish genetic differences.

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Ahh, I gotcha.What you should be looking for is mutation rates. Not only mutation rates, but the mutation rate of "junk DNA" vs. "transcribed DNA". Throughout genetics, it is observed that non-transcribed, non-regulatory DNA (ie junk DNA) contains more differences than transcribed DNA between species who share a recent common ancestor. This allows us to roughly estimate the occurrence of neutral and beneficial mutations within transcribed DNA. It is a very rough estimate, but junk DNA almost always contains more mutations than transcribed DNA, as would be expected.But this isn't the whole enchilada. The second mode of evolution, outside of mutation and selection, is speciation. This is a little harder to map. Mutations happen in a somewhat clockwork fashion. Speciation can happen quickly or not at all, depending on the situation. Mutations are related to biochemical processes while speciation relies on the environment and genetic flow within the population.Perhaps a good place to look is in comparing relatively stable environments with little immigration, such as the American Prairie, and areas with sudden immigration. One such place/species group are the cichlids. These fish speciated quickly once they entered into the Lake Victoria complex. Some estimate the number of new species at 250+, all of which occurred in less than 250,000 years. However, all 250 species differ very little genetically. This is in contrast to a more stable environment where species share far less genetic similarity and more distant common ancestors.I really don't have that many references on cichlids, so much of this is from memory. I do remember enough to know that this might fit into your ideas. Anyone else have good references for cichlids?

It may be that my question isn't answerable right now.When we look at extant life do we see any huge chasms anywhere?Of course, if we pick an oak tree and an aardvark the genetic difference is very large. Is there, however, a path of organisms that are currently alive that connects the two without any very large chasms?It seems to me that the path would trace back toward organisms that are somewhat like (genetically) the last common ancestor of them both.Am I making sense yet? I'm looking for a small step path through "gennome space" in extant creatures.

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When we look at extant life do we see any huge chasms anywhere?

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Boy, you really are going back to basics.The biggest division I see is the divide between prokaryote and eukaryote. This division was not caused by natural selection and mutation directly, but rather through endosymbiosis. The mitochondria, and later in plants the chloroplast, are captured organisms that made eukaryotes possible. The organisation of the nucleus and cytoplasmic space are also hurdles that may have been crossed through endosymbiosis. However, the root of the whole eukaryotic clade could have been a one time event, the engulfment of another organism. IMHO, the divide between plants and animals is not nearly as wide as the divide, or chasm, between prokaryotes and eukaryotes.

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Of course, if we pick an oak tree and an aardvark the genetic difference is very large. Is there, however, a path of organisms that are currently alive that connects the two without any very large chasms?

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I wrote a whole paragraph on "what I don't know about basal eukaryotes" before I started looking around and found the answer. That, and I hit myself in the head for forgetting the my first semester of Zoology class. The common ancestor to both plants and animals are (according to evolutionary theory) protists. Extant organisms include amoebas, euglenia, and quite a few others. Read more here: Introduction to the Basal EukaryotesABE: The homepage (Tree of Life Web Project) might be useful as well. I haven't looked at it in depth, but it seems pretty accurate and basic.ABE, again: Dammit, I no sooner post an edit than I find the answer you are looking for. Below are two trees that give the realationship between the major lineages (two different views). All of life can be categorized by one of those headings. You will notice that where the clades intersect there is not a lineage given. This is because there are no representatives of that common ancestor. For example, in the archaea tree, there is not an extant (or fossil I presume) species representing the common ancestor of eubacteria, archae, and eukaryotes. These are the chasms that you want to know about.The graph transfered over as ASCII. Check it out here: Life on EarthThis message has been edited by Loudmouth, 01-11-2005 20:47 AMThis message has been edited by Loudmouth, 01-11-2005 20:54 AM

{disregard}This message has been edited by TheLiteralist, 01-12-2005 02:14 AM

{disregard}This message has been edited by TheLiteralist, 01-12-2005 02:15 AM

This is NOT the place for those questions NOR I will note the answers.Thank you for sticking to a very narrow topic.

I thought it fit in, but who would know better than the one who wrote the opening post?I can always start a thread with those questions later.No problem...I'd hate to see my thread get shifted out to left field somewhere.I deleted my posts, if that's okay.This message has been edited by TheLiteralist, 01-12-2005 02:19 AM