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Author | Topic: Potential falsifications of the theory of evolution | |||||||||||||||||||||||||||||||||||||||
Percy Member Posts: 22480 From: New Hampshire Joined: Member Rating: 4.8 |
Hi Dwise1,
I haven't been following your exchange with WK, but if you're looking for the MA source files then go to that link you mentioned:
Click on "Linux Source Distribution". Download and unpack mendel_v1.4.7.tar.gz. It contains all the sources, here's the index:
sh-3.2$ gzip -d -c mendel_v1.4.7.tar.gz.gz | tar -tf - mendel_v1.4.7/ mendel_v1.4.7/version mendel_v1.4.7/favicon.ico mendel_v1.4.7/html/ mendel_v1.4.7/html/images/ mendel_v1.4.7/html/images/mendel.png mendel_v1.4.7/html/images/logo.png mendel_v1.4.7/html/account.html mendel_v1.4.7/html/intro.html mendel_v1.4.7/html/tips.html mendel_v1.4.7/html/tips.js mendel_v1.4.7/html/other.html mendel_v1.4.7/html/toc.html mendel_v1.4.7/html/index.html mendel_v1.4.7/cgi-bin/ mendel_v1.4.7/cgi-bin/cmendel.exe mendel_v1.4.7/cgi-bin/fmendel.exe mendel_v1.4.7/cgi-bin/cmendel/ mendel_v1.4.7/cgi-bin/cmendel/CVS/ mendel_v1.4.7/cgi-bin/cmendel/CVS/Repository mendel_v1.4.7/cgi-bin/cmendel/CVS/Entries mendel_v1.4.7/cgi-bin/cmendel/CVS/Root mendel_v1.4.7/cgi-bin/cmendel/diagnostics.c mendel_v1.4.7/cgi-bin/cmendel/Makefile mendel_v1.4.7/cgi-bin/cmendel/config.h mendel_v1.4.7/cgi-bin/cmendel/debug.c mendel_v1.4.7/cgi-bin/cmendel/fileio.c mendel_v1.4.7/cgi-bin/cmendel/init.c mendel_v1.4.7/cgi-bin/cmendel/mem.c mendel_v1.4.7/cgi-bin/cmendel/mendel.c mendel_v1.4.7/cgi-bin/cmendel/mendel.h mendel_v1.4.7/cgi-bin/cmendel/mendel.in mendel_v1.4.7/cgi-bin/cmendel/mpi.c mendel_v1.4.7/cgi-bin/cmendel/offspring.c mendel_v1.4.7/cgi-bin/cmendel/ranlib.c mendel_v1.4.7/cgi-bin/cmendel/ranlib.h mendel_v1.4.7/cgi-bin/cmendel/readme mendel_v1.4.7/cgi-bin/cmendel/selection.c mendel_v1.4.7/cgi-bin/cmendel/sort.c mendel_v1.4.7/cgi-bin/cmendel/.#sort.c.1.2 mendel_v1.4.7/cgi-bin/fmendel/ mendel_v1.4.7/cgi-bin/fmendel/CVS/ mendel_v1.4.7/cgi-bin/fmendel/CVS/Root mendel_v1.4.7/cgi-bin/fmendel/CVS/Repository mendel_v1.4.7/cgi-bin/fmendel/CVS/Entries mendel_v1.4.7/cgi-bin/fmendel/Makefile mendel_v1.4.7/cgi-bin/fmendel/common.h mendel_v1.4.7/cgi-bin/fmendel/mendel.f mendel_v1.4.7/cgi-bin/fmendel/mendel.in mendel_v1.4.7/cgi-bin/fmendel/mpi_mendel.f mendel_v1.4.7/cgi-bin/fmendel/mpi_mendel_seq.f mendel_v1.4.7/cgi-bin/fmendel/pbs.script mendel_v1.4.7/cgi-bin/fmendel/random_pkg.f90 mendel_v1.4.7/cgi-bin/fmendel/sort.f90 mendel_v1.4.7/cgi-bin/plot_recipes.cgi mendel_v1.4.7/cgi-bin/config.inc mendel_v1.4.7/cgi-bin/delete.cgi mendel_v1.4.7/cgi-bin/diff.cgi mendel_v1.4.7/cgi-bin/label_post.pl mendel_v1.4.7/cgi-bin/list_cases_win.cgi mendel_v1.4.7/cgi-bin/monitor.ajax mendel_v1.4.7/cgi-bin/list_cases.cgi mendel_v1.4.7/cgi-bin/qsub.pl mendel_v1.4.7/cgi-bin/list_files.cgi mendel_v1.4.7/cgi-bin/Makefile mendel_v1.4.7/cgi-bin/mendel.in mendel_v1.4.7/cgi-bin/mendel.in.yeast mendel_v1.4.7/cgi-bin/more.cgi mendel_v1.4.7/cgi-bin/readme mendel_v1.4.7/cgi-bin/qdel.cgi mendel_v1.4.7/cgi-bin/output.cgi mendel_v1.4.7/cgi-bin/plot_modify.cgi mendel_v1.4.7/cgi-bin/memory.inc mendel_v1.4.7/cgi-bin/plots.cgi mendel_v1.4.7/cgi-bin/start.cgi mendel_v1.4.7/cgi-bin/qmpd.cgi mendel_v1.4.7/cgi-bin/qstat_main.cgi mendel_v1.4.7/cgi-bin/qstat.cgi mendel_v1.4.7/cgi-bin/with_selected.cgi mendel_v1.4.7/cgi-bin/parse.inc mendel_v1.4.7/cgi-bin/rename.cgi mendel_v1.4.7/cgi-bin/monitor.cgi mendel_v1.4.7/cgi-bin/input_file_reader.inc mendel_v1.4.7/cgi-bin/label_form.cgi mendel_v1.4.7/cgi-bin/input_file_writer.pl mendel_v1.4.7/cgi-bin/plots_combine.cgi mendel_v1.4.7/cgi-bin/input_file_parser.inc mendel_v1.4.7/cmendel mendel_v1.4.7/fmendel mendel_v1.4.7/js/ mendel_v1.4.7/js/tabpane.js mendel_v1.4.7/js/jquery.js mendel_v1.4.7/js/stylize_buttons.js mendel_v1.4.7/js/flot/ mendel_v1.4.7/js/flot/examples/ mendel_v1.4.7/js/flot/examples/basic.html mendel_v1.4.7/js/flot/examples/layout.css mendel_v1.4.7/js/flot/examples/zooming.html mendel_v1.4.7/js/flot/examples/graph-types.html mendel_v1.4.7/js/flot/examples/selection.html mendel_v1.4.7/js/flot/examples/setting-options.html mendel_v1.4.7/js/flot/examples/index.html mendel_v1.4.7/js/flot/examples/dual-axis.html mendel_v1.4.7/js/flot/examples/interacting.html mendel_v1.4.7/js/flot/examples/time.html mendel_v1.4.7/js/flot/examples/visitors.html mendel_v1.4.7/js/flot/examples/turning-series.html mendel_v1.4.7/js/flot/examples/mendel.html mendel_v1.4.7/js/flot/excanvas.pack.js mendel_v1.4.7/js/flot/excanvas.js mendel_v1.4.7/js/flot/TODO mendel_v1.4.7/js/flot/API.txt mendel_v1.4.7/js/flot/NEWS.txt mendel_v1.4.7/js/flot/README.txt mendel_v1.4.7/js/flot/jquery.flot.js mendel_v1.4.7/js/flot/jquery.flot.pack.js mendel_v1.4.7/js/flot/jquery.js mendel_v1.4.7/js/flot/index.html mendel_v1.4.7/css/ mendel_v1.4.7/css/style1.css mendel_v1.4.7/css/style2.css mendel_v1.4.7/css/tab.webfx.css mendel_v1.4.7/css/form.css mendel_v1.4.7/images/ mendel_v1.4.7/images/nodata.html mendel_v1.4.7/images/mendel_logo.png mendel_v1.4.7/images/nodata.png mendel_v1.4.7/images/mendel.png mendel_v1.4.7/images/logo.png mendel_v1.4.7/images/button.gif mendel_v1.4.7/images/famfamfam.com/ mendel_v1.4.7/images/famfamfam.com/application_go.png mendel_v1.4.7/images/famfamfam.com/cross.png mendel_v1.4.7/images/famfamfam.com/page_white_get.png mendel_v1.4.7/images/famfamfam.com/page_white_put.png mendel_v1.4.7/images/famfamfam.com/folder_page.png mendel_v1.4.7/images/famfamfam.com/chart_curve.png mendel_v1.4.7/images/famfamfam.com/folder_explore.png mendel_v1.4.7/images/famfamfam.com/information.png mendel_v1.4.7/images/famfamfam.com/world_link.png mendel_v1.4.7/images/famfamfam.com/user.png mendel_v1.4.7/images/famfamfam.com/comment.png mendel_v1.4.7/images/famfamfam.com/arrow_branch.png mendel_v1.4.7/images/famfamfam.com/delete.png mendel_v1.4.7/images/famfamfam.com/textfield_rename.png mendel_v1.4.7/images/famfamfam.com/lock.png mendel_v1.4.7/images/famfamfam.com/tick.png mendel_v1.4.7/images/famfamfam.com/time_add.png mendel_v1.4.7/images/famfamfam.com/compress.png mendel_v1.4.7/images/famfamfam.com/lock_open.png mendel_v1.4.7/help.html mendel_v1.4.7/Makefile mendel_v1.4.7/configure mendel_v1.4.7/README mendel_v1.4.7/win/ mendel_v1.4.7/win/in.nsi mendel_v1.4.7/index.html You can also just say "tar -tzf mendel_v1.4.7.tar.gz.gz" if you have a gzip capable version of tar. --Percy
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Percy Member Posts: 22480 From: New Hampshire Joined: Member Rating: 4.8 |
Hi Crash!
I think we think about design the same way, but I thought I'd make sure.
crashfrog writes: Sure, there's design in places in the biological world. Most species show absolutely no design of any kind, at all. And the few species that do - agricultural cultivars, livestock, de novo proteins, GM organisms, bespoke bacteria, and the like - were designed by human beings. Naturally, all these organisms are no older than human civilization. There are no examples of design in organisms prior to when humans began to design organisms. When you say design I think you mean design with purpose and intent by some tangible entity, is that right? If so, then I think we're on the same page. But there can also be unintended design. Current theories about the origin of agriculture are that each new season men would only plant grain that they found most advantageous the previous season, thereby unintentionally carrying out breeding experiments. Then there are those strange Japanese crabs with the outline of a warrior on their carapace created by an unintentional breeding program driven by superstition. So I often find it effective to concede that there is indeed design everywhere throughout nature, but that the process of descent with modification and natural selection is the designer. Evolution finely crafts the adaptation of organisms to their environment that has all the appearance of being purposefully designed. We don't have to agree on this, but just thought I'd bring it up in case it helps with AOK. --Percy
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dwise1 Member Posts: 5948 Joined: Member Rating: 5.5 |
Which is exactly what I did. On 02 Nov 2010 at 1312 PDT. However, the file they had up at that time was 484 KB in size (at least that's what my file manager reports), whereas they now list it as being 1.1 MB in size. When did you and WK download it?
I'll try downloading it yet again tonight. Right now I need to hit the road for a 2 hour drive to an all-day seminar, followed by a 2 hour drive home, so that will be contingent on my condition when I return.
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Percy Member Posts: 22480 From: New Hampshire Joined: Member Rating: 4.8 |
dwise1 writes: ...so that will be contingent on my condition when I return. Hopefully returning itself will be "contingent on my condition." I know you said "seminar," but there's always that unwinding period in the bar at the end of the day. Have fun but be safe. --Percy
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dwise1 Member Posts: 5948 Joined: Member Rating: 5.5 |
No, no bar involved. I don't frequent bars, or even occasion them. Rather what with getting up extra early and then sitting through 7 hours of presentations (only a quarter of which applied to me), I wasn't sure that I'd be able to stay awake during the two-hour drive back. Didn't have any problem, though.
Still no luck with that tarball. The -tf option for tar does display the source files, but not extract them. Neither does the -xf option.
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Percy Member Posts: 22480 From: New Hampshire Joined: Member Rating: 4.8 |
dwise1 writes: Still no luck with that tarball. The -tf option for tar does display the source files, but not extract them. Neither does the -xf option. The "t" in "tar -tf" stands for "table of contents," so it will only display what is in the tarball. The "x" in "tar -xf" stands for "eXtract", and should extract all files, including the source files. Are you saying it extracts other files but not the source files? Or is it extracting nothing? You should see a top level directory called "mendel_v1.4.7", and it should contain everything listed in the table of contents. Are you using true Linux or at least Unix, or are you using an emulator? --Percy
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dwise1 Member Posts: 5948 Joined: Member Rating: 5.5 |
Have you actually extracted those source files? -t displayed those files, but -x didn't extract them. Could it do that for you?
I have Ubuntu running under VMWare on my Win7 box, Kosmic Koala. Previously, I had community college classes with RedHat 6 (upwards of 8 years ago) and up until 3 or 4 years ago used to have a Linux box at work running RedHat 7. I was going to wait until firing up my WinXP laptop tomorrow which has WinZIP on it (my Win7 box does not), but I just now took another look. Here is the directory listing from Ubuntu:
quote: On the SourceForge site, the Linux file was listed as having a size of 1.1 MB, but the file I downloaded is a tenth of that size -- and it is a fourth of the size of the "old" file I had previously downloaded. That "new" smaller file did report source files with -t, but allowed none to be extracted.
Whisky-Tango-Foxtrot-Oscar? What does ls -al have to say about the tarball you downloaded? How big is it? Were you ever able to actually extract any source files from it?
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Percy Member Posts: 22480 From: New Hampshire Joined: Member Rating: 4.8 |
I can open and examine all the files. There are source files in Perl, Fortran, HTML, Javascript and CSS. Let me repeat the process and see if I can download and unpack it again.
First I go to Mendel’s Accountant download | SourceForge.net Then I click on the "View all files" button. Then I click on "Linux Source Distribution". Then I click on "mendel_v1.4.7.tar.gz", which for me downloads the file "mendel_v1.4.7.tar.gz.gz", which is fine. I move the the downloaded file from my Windows machine to my Linux machine and put it in a temp directory. I execute this command: tar -xzf mendel_v1.4.7.tar.gz.gz It extracts the directory mendel_v1.4.7 and all it's contents. I do an ls on the directory:
% ls -l mendel_v1.4.7 total 176 -rw-r--r-- 1 elkind cadence10 6650 Jul 23 2009 Makefile -rw-r--r-- 1 elkind cadence10 2524 Jul 23 2009 README drwxr-xr-x 4 elkind cadence10 4096 Jul 23 2009 cgi-bin lrwxrwxrwx 1 elkind cadence10 15 Nov 8 08:13 cmendel -> cgi-bin/cmendel -rwxr-xr-x 1 elkind cadence10 29111 Jul 23 2009 configure drwxr-xr-x 2 elkind cadence10 4096 Jul 23 2009 css -rw-r--r-- 1 elkind cadence10 9662 Jul 23 2009 favicon.ico lrwxrwxrwx 1 elkind cadence10 15 Nov 8 08:13 fmendel -> cgi-bin/fmendel -rw-r--r-- 1 elkind cadence10 88443 Jul 23 2009 help.html drwxr-xr-x 3 elkind cadence10 4096 Jul 23 2009 html drwxr-xr-x 3 elkind cadence10 4096 Jul 23 2009 images -rw-r--r-- 1 elkind cadence10 165 Jul 23 2009 index.html drwxr-xr-x 3 elkind cadence10 4096 Jul 23 2009 js -rw-r--r-- 1 elkind cadence10 16 Jul 23 2009 version drwxr-xr-x 2 elkind cadence10 4096 Jul 23 2009 win I do an ls on one of the subdirectories:
% ls -l mendel_v1.4.7/js total 80 drwxr-xr-x 3 elkind cadence10 4096 Jul 23 2009 flot -rw-r--r-- 1 elkind cadence10 55774 Jul 23 2009 jquery.js -rw-r--r-- 1 elkind cadence10 873 Jul 23 2009 stylize_buttons.js -rw-r--r-- 1 elkind cadence10 10182 Jul 23 2009 tabpane.js I cat the smallest file:
% cat mendel_v1.4.7/js/stylize_buttons.js /** this plugin converts ugly submit buttons to nice looking buttons see: http://www.oscaralexander.com/tutorials/how-to-make-sexy-buttons-with-css.html This jQuery plugin is created by Jankees van Woezik for www.base42.nl Date: October 3, 2008 */ jQuery.fn.stylizeButton = function() { return this.each(function(){ //value is the text in the button var value = this.value; var id = this.id; if($(this).attr("stylizeAction") == "submit"){ $(this).css({ display:"none"}); $(this).after(""+value+""); }else if($(this).attr("stylizeAction") == "clean"){ $(this).css({ display:"none"}); $(this).after(""+value+""); }else{ //sorry for now i only do submit buttons and clean buttons } }); }; The download and unpacking seems to be okay. I haven't attempted building it. --Percy
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NoNukes Inactive Member |
If you do tar -xf blah.tar, the files will be extracted but nothing will be displayed on screen at least with gnu tar.
Try adding the 'v' for verbosity option. tar -xvf blah taror tar -xzvf blah.tar.gz Edited by NoNukes, : No reason given.
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AlphaOmegakid Member (Idle past 2897 days) Posts: 564 From: The city of God Joined: |
This is just a restatement of the original statement that I questioned. Again, just how do you envision this happening? Yes, slightly deleterious alleles can become fixed in a population, but you go beyond Kimura and Ohta in claiming that deleterious genes must inevitably accumulate in populations to the point of making them less fit than prior generations. This is not a valid extrapolation of Kimura and Ohta. Here's why you're wrong: Imagine you have a population with slightly deleterious allele X that is not affected by natural selection and that eventually becomes fixed. Later slightly deleterious allele Y occurs in a different gene. It, too, is unaffected by natural selection, even in combination with allele X, and it, too, eventually becomes fixed in the population. Still later, slightly deleterious allele Z occurs in a different gene. It, too, is unaffected by natural selection, even in combination with alleles X and Y, and it, too, eventually becomes fixed in the population. This population can go on accumulating and fixating slightly deleterious alleles that are unaffected by natural selection even in combination with all the other deleterious alleles, and since there is no impact on natural selection then there cannot possibly be any impact on fitness. As soon as you introduce a slightly deleterious allele into the population that in combination with the older and now fixated deleterious alleles is subject to natural selection because it diminishes fitness, then that allele will be selected against. It will not spread through the population and cause the population to be less fit than prior generations. You are dancing all around the obvious without seeing the consequences. X, Y, and Z are slightly deleterious in your scenario. By definition, that means that there is a fitness decrease already. How did they become fixed then? Well, the negative effect on the phenotype was so small that in nature there was no recognizable fitness difference between thiose organizms that had X, Y, and Z slightly deleterious alleles and so the population frequency of those alleles increased through drift. Now you also need to realize that the ancestrasl population did not have slightly deleterious mutations X, Y, and Z. Therefore their relative fitness is higher than the XYZ drifted population. Now in your last paragraph is where you make your mistake. Fitness is not dependant on natural selection. In fact, it must be totally independant. Random mutation happens in populations with or without selection. Let's reduce NS too zero (or as close as possible). Let's in the lab supply an environment where there are no predators, plenty of food, and a viable climate. The populations will thrive, Right? But each generation will have more mutations that the ancestral populations. The fitness will decline relative to the ancestral population. This is a fact. No we allow for NS. The same mutations are randomly happening at the same rate. We put them back in to an environment where the have to struggle for food, escape predators, and fight the environment. Some will die. The weakest supposedly. And the strongest survive. But the strongest have more mutations than the ancestral population. They are indeed the most fit in that generation, but they are not the most fit relative to their ancestral population. And each generation gets progressively worse. The only way this can succeed is if the population is drastically declined to a few who have some benefical mutations which out weigh the slightly deleterious ones. We see this all the time in bacteria. We place them in an environment where the whole population dies except a few and then we see the bacteria thriving once again. Bacteria and viruses and the like can afford these drastic bottlenecks (they can afford the cost of selection). However when you have sexual creatures, they rarely can go through these bottlenecks with out severe genetic drift problems which show up in inbreeding depression. They also rarely see these bottleneck reductions in reality. Those that do are on the endangered species list, and need our help in manipulating NS. Now keep in mind, the problem is not the population size as most think it is. The problem is the frequency of alleles in the population, whatever the size. Many bottlenecks survive and do just fine (island populations(for a while)). But many do not (endangered species). The problem is not the population size. The problem is the frequency of deleterious mutation in the population. When the frequency of deleterious mutations is high, then homozygosity of those alleles gets expressesd and NS has a hay day. When the frequency of deleterious alleles is low, then heterozygosity reigns and the population diverges, but successfully.
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Coyote Member (Idle past 2127 days) Posts: 6117 Joined: |
So how many generations does it take for extinction?
300 generations? 6,000 years? Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.
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Wounded King Member Posts: 4149 From: Cincinnati, Ohio, USA Joined: |
Fitness is not dependant on natural selection. In fact, it must be totally independant. This simply makes no sense., in the first place both fitness and natural selection are heavily determined by the environmental context of an organism to consider them totally independent is to ignore reality. Since we accept that drift can change fitness contrary to the tendencies of natural selection we can acknowledge that NS does not directly dictate changes in fitness in every instance so that fitness is not strictly dependent on NS, but to suggest they are totally independent is simply wrong. You seem to be claiming that NS has no influence on fitness, how can you possibly make a case for this, rather than just claiming it with no justification. I'm also not sure what you think your experiment demonstrates, that adaptation to a permissive environment does not well adapt you for a restrictive environment? Well, gosh, I'm totally shocked by your radical new idea. It certainly doesn't demonstrate that the more recent population is absolutely less fit than the ancestral one, just that it is less fit in the environment the ancestor was already adapted to. The real way to test the comparative fitness would be a cross evnvironmental comparison of the derived and ancestral strains in the permissive and restrictive environments. If the ancestral strain was fitter in both environments then you could make your case, on the other hand if the derived line was fitter in the permisive environment all you would have shown is adaptation in action. You need to bear in mind that your idea of totally removing NS is simply impossible unless you artificially enforce your organisms to all have the same number of offspring, and even then you can't get around selection against totally lethal mutations. The only fitness that seems to be declining in your example is their fitness for an environment they are no longer in. Many mutations deleterious in a restrictive environment may be beneficial in the permissive environment, as is seen when bacteria in a permissive environments lose unnecessary biosynthesis pathways, or in the case of antibiotic resistant strains that are less fit than the wild type in the absence of antibiotic. Conversely in some antibiotic selection experiments resistant mutations can be identified which are fitter than the Wild Type even in a permissive environment (Kassen and Bataillon, 2006). I suggest that rather than the deleterious mutation rate the true key element is the overall distribution of fitness effects, you can't debate this meaningfully while simply pretending that advantageous and indeed slightly advantageous mutations don't exist which can counteract the fitness effects of deleterious mutations. TTFN, WK
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AlphaOmegakid Member (Idle past 2897 days) Posts: 564 From: The city of God Joined: |
So how many generations does it take for extinction? 300 generations? 6,000 years? That depends on.... The effective population sizeThe mutation rate the ratio of beneficial mutations to non beneficial The genome size The number of linkage units The strength of natural selection And one of the most important is the number of offspring per generation And there are other variables as well such as heritability, ratio of recessives, etc. Let me know the variables and I can give you an answer.
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Dr Adequate Member (Idle past 305 days) Posts: 16113 Joined: |
That depends on.... The effective population sizeThe mutation rate the ratio of beneficial mutations to non beneficial The genome size The number of linkage units The strength of natural selection And one of the most important is the number of offspring per generation And there are other variables as well such as heritability, ratio of recessives, etc. Let me know the variables and I can give you an answer. Um ... but in the real world genetic meltdown doesn't actually happen. You can't expect us to make up the numbers that support your fantasy. Being wrong about genetics is your job.
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Coyote Member (Idle past 2127 days) Posts: 6117 Joined: |
So how many generations does it take for extinction? 300 generations? 6,000 years? That depends on.... The effective population sizeThe mutation rate the ratio of beneficial mutations to non beneficial The genome size The number of linkage units The strength of natural selection And one of the most important is the number of offspring per generation And there are other variables as well such as heritability, ratio of recessives, etc. Let me know the variables and I can give you an answer. Here's the bottom line: life has been around for several billion years and it hasn't succumbed to "genetic entropy" yet. I don't think we have to worry much about it. I think the reason creationists have jumped on this bandwagon is 1) a religious belief in "the fall" and 2) a religious belief in a young earth. Both are myths, and have no place in science, but that is apparently what is behind this nonsense. Unless you have evidence? If so I would love to see it. Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.
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