tag:blogger.com,1999:blog-37148773.post764202656128772352..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: What's in Your Genome? Chapter 4: Pervasive TranscriptionLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger200125tag:blogger.com,1999:blog-37148773.post-42168778666666481702017-03-29T15:07:16.978-04:002017-03-29T15:07:16.978-04:00TX, your latest response involves several differen...TX, your latest response involves several different thoughts mixed together. They're easier to deal with if we look at them in turn.<br /><br />1. My point about flightlessness and blind cave animals is that LOSS of a trait is genetically easy, as explained above. This should be obvious. <br /><br />2. Many birds that are not ratites also lost flight. Examples include many rails, a cormorant, a parrot, weird pigeon relatives, a few ducks, an auk, penguins, etc. Therefore, the evolution of flightlessness is not equal to the evolution of ratites.<br /><br />3. Birds can travel from one continent to another, or to islands, in two main ways. They can make one long flight. Also, if they can take off from water, they can fly a while, rest, fly some more. (They can also be blown off course by storms, or raft on vegetation, like mammals.) Therefore, it isn't surprising that sometimes -- at least occasionally -- some birds cross water barriers.<br /><br />4. The ancestors of ratites could fly. Some ratites (tinamous) can fly now. It's entirely plausible that ancestors of current ratites crossed water barriers by flying, and evolved flightlessness afterwards. The different forms of their wings seem to suggest this.<br /><br />5. Each time we discuss flightlessness, you pull gigantism into the discussion. They aren't the same. While it is true that giant birds are probably too big to fly, many flightless birds are small enough that weight alone doesn't prevent flight (kiwi, cormorant, parrot, rails, etc.).<br /><br />6. Gigantism is an interesting trait itself, and it does seem to have evolved convergently in some of the surviving lineages of ratites (but not kiwis or tinamous). It has also evolved in elephants, giraffes, whales, and numerous extinct mammals. I don't know how it evolves. I don't know if early ancestors of ratites had traits that made evolving larger size particularly easy for them, or if conditions after the extinction of non-avian dinosaurs opened an ecological niche for large dinosaur descendents and the proto-ratites were in the right place at the right time. It would be interesting to know, and I hope someone finds out.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-3545115065521605262017-03-29T07:35:03.511-04:002017-03-29T07:35:03.511-04:00Tx:
"But the new, and curiously similar, feat...Tx:<br />"But the new, and curiously similar, features evolving on different continents taxes the random development idea."<br />It's quite obvious only you find this taxing. What you don't seem to find taxing is how did kangaroos end up in Australia when Noahs arc landed somewhere in the middle east a few thousand years ago? And the splitting of the continents happend hundreds million years ago.<br />Did the 'roo's hitch a ride on branches floating to down under?Edhttps://www.blogger.com/profile/15924368353226400878noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-64604990325855792502017-03-29T01:22:22.207-04:002017-03-29T01:22:22.207-04:00bwilson295,
“However, if the birds don't need...bwilson295,<br /><br />“However, if the birds don't need to fly, individuals showing such mutations don't die. They can reproduce.”<br /><br />Yeah, I understand why that makes sense to you. But the new, and curiously similar, features evolving on different continents taxes the random development idea. Did they evolve the size, bone mass and all the other stuff while their wings were becoming vestigial, or did one feature kinda play into some kind of selection pressure for the others? (Just below convergent evolution, parallel accidental development is my favorite evolutionary concept. It generates all kinds of interesting questions like how the ten layers of your retinas accidentally developed, or ditto for the water/oil/mucus tears that, with the indispensable help of your accidental eyelids, do all kinds of stuff to protect and maintain your corneas.) <br /><br />But those things aside, and speaking of the breakup of Gondwana, when would you suppose those DNA replication errors started coming into play? Was it when the severed segments of Gondwana were 500 yards apart, or 100 miles? There must have been a time when they were only a few feet away, and the flighted ancestors could still move back and forth. But there would have come a time when intercontinental flight would have been very difficult for an evolving population, or even a breeding pair. I’m thinking that some of the rainy-day mutations must have already been in the pool, but it is real mess to think about. When you're reading about blue-ribbon phylogenetic breakthroughs, do you wonder about stuff like that?<br /><br />Oh, one more question. Moas apparently lost their wings without leaving so much as a vestigial trace. How and why would you suppose that happened?txpiperhttps://www.blogger.com/profile/03645156881353741058noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-85642664347067158642017-03-28T13:55:24.120-04:002017-03-28T13:55:24.120-04:00Once again, we see the intellectual inconsistency ...Once again, we see the intellectual inconsistency of creationism. "Evolution can't happen, 'cuz all mutations are destructive. Beneficial mutations never happen." That's what they usually say. Except when confronted with something like the loss of flight or vision. Then the story suddenly becomes "How could such destructive mutations happen?"<br /><br />One wonder how their brains don't explode from holding so many mutually contradictory beliefs. Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-44417071551972035972017-03-28T13:49:16.034-04:002017-03-28T13:49:16.034-04:00TX, mutations that reduce or eliminate the ability...TX, mutations that reduce or eliminate the ability to fly occur in all populations of flying birds. If the individuals showing such mutations really need to fly, what happens to them?<br /><br />They die. They're eaten by predators or they can't find food. Their flight-reducing mutations never become common in the population (though if these mutations are recessive, they may remain in the population, as "standing variation").<br /><br />However, if the birds don't need to fly, individuals showing such mutations don't die. They can reproduce. The mutations can become common in the population. In fact, they may be favored because the birds save the energy used to make big wings. <br /><br />Therefore, the evolution of flightlessness in ratites, ducks, a parrot, a cormorant, and several rails is not a spooky coincidence. It's a likely result of the many different mutations that can cause flightlessness, under situations where flightlessness is harmless. Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-44163878409270685462017-03-28T11:57:58.111-04:002017-03-28T11:57:58.111-04:00So, Bill, are you saying we have no direct evidenc...<i>So, Bill, are you saying we have no direct evidence that heritable morphological change is due to mutations?</i><br /><br />Not Bill, but my supposition is this is the well worn trope we've gone over before, that eventually evolution reduces to a tautology. So of course the folks who make much of this trope call it a "mere" tautology, or "circular reasoning."<br /><br />The major problem with this way of thinking is that *any* true statement logically reduces to a tautology. (E.g., two squared equals four, which reduces to four equals four.) <br /><br />So ability to reduce something to a tautology simply proves a statement is true. (Bill, you paying attention?) The much more better question is whether one or more of the various ways in which the truth can be stated are enlightening, and that is surely true of evolution.judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-42937346751157649762017-03-28T11:52:44.641-04:002017-03-28T11:52:44.641-04:00fantastic coincidental failures
Neither. Random ...<i>fantastic coincidental failures</i><br /><br />Neither. Random failures at well established rates. And nothing coincidental about them. Different loss-of-function failures, as the study that G M-H referenced demonstrated so well.judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-19034081041119781712017-03-28T11:50:28.612-04:002017-03-28T11:50:28.612-04:00So, Bill, are you saying we have no direct evidenc...So, Bill, are you saying we have no direct evidence that heritable morphological change is due to mutations? You're even more ignorant than I feared.<br /> Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-20515232278313900282017-03-28T11:31:34.783-04:002017-03-28T11:31:34.783-04:00LS
"What do you think happens instead, Bill? ...LS<br />"What do you think happens instead, Bill? Does Baby Jesus sneak about in the night plucking the feathers from the wings of each individual bird so they can't fly?"<br /><br />So the current explanation, based on circular reasoning sucks, but it's the best we have :-)Bill Colehttps://www.blogger.com/profile/06642212549806694659noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-31711550415446300582017-03-28T01:41:06.313-04:002017-03-28T01:41:06.313-04:00bwilson295,
“Many, many genes can damage or destr...bwilson295,<br /><br />“Many, many genes can damage or destroy a complex trait.”<br /><br />“Our understanding of ratite evolution has improved in several steps. Current thinking definitely is that ancestral members of the clade could fly…”<br /><br />Yeah, but don’t you see what all you’re dealing with here? In the first place, the mutations that you believe produced those many, many flight associated genes (you want to talk about how random mutations produced those genes?) are now credited with fantastic coincidental failures. And more accidental genes, or accidentally altered genes, are supposed to have popped the hell up out of nowhere in descendants in Africa, Australia, South America, New Zealand and Madagascar to produce giant flightless birds with all kinds of variant traits. Thickened bones, increased body mass, foot alterations, etc. <br /><br />You have matchless faith in DNA replication errors occurring in the same genes, that might occur in the rarest of germ cells which might be involved in reproduction and might wind up fixed in a population. All ridiculously low-probability events, but you believe things like this happened billions of times with monotonous regularity. Really impressive faith and reverence, but not at all believable.txpiperhttps://www.blogger.com/profile/03645156881353741058noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-11174661295746976032017-03-27T17:08:05.154-04:002017-03-27T17:08:05.154-04:00bw,
Sounds reasonable. I like reading those answer...bw,<br />Sounds reasonable. I like reading those answers myself. I've learned a thing or two about studies I had not checked before.Gabohttps://www.blogger.com/profile/17552375541700079254noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-53778234180061516472017-03-27T16:56:17.611-04:002017-03-27T16:56:17.611-04:00G M-H, it's clear that responding to TX has no...G M-H, it's clear that responding to TX has no direct good effect, but still I respond sometimes, for two reasons. First, writing this stuff is fun. Second, others who aren't commenting may be learning at lot more than TX.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-14101070668199574932017-03-27T16:16:21.080-04:002017-03-27T16:16:21.080-04:00@ Bill Cole
Can you identify the mutations that c...@ Bill Cole<br /><br /><i>Can you identify the mutations that caused the loss of flight in any of these birds?</i><br /><br />What do you think happens instead, Bill? Does Baby Jesus sneak about in the night plucking the feathers from the wings of each individual bird so they can't fly?Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-81849047143752832462017-03-27T16:08:25.872-04:002017-03-27T16:08:25.872-04:00Take a look at this picture showing the location o...Take a look at this picture showing the location of different kinds of mutations in the CTFR gene, the gene that can cause cystic fibrosis if mutated (depending on what effect the mutation has). <br /><br />http://www.genet.sickkids.on.ca/PicturePage.html<br /><br />The top line is a simplified map of the gene. The other lines show locations of mutations that have been detected in humans. The bottom line ("seq. var.") are harmless mutations. The others cause mild to severe disease. <br /><br />Many, many mutations can occur in this one gene in humans! <br /><br />Complex organs, like eyes or wings, involve input from many genes, and each can mutate at any point. <br /><br />Evolution of LOSS of a complex organ or function is not difficult, assuming the organism can survive without it. Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-80155094837424725392017-03-27T15:53:40.640-04:002017-03-27T15:53:40.640-04:00Nah, what Bill wants is a play by play replay of t...Nah, what Bill wants is a play by play replay of the events leading to loss of sight, or else goddidit.Edhttps://www.blogger.com/profile/15924368353226400878noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-51832249474900338192017-03-27T14:59:42.773-04:002017-03-27T14:59:42.773-04:00"Can you identify the mutations that caused t..."Can you identify the mutations that caused the loss of flight in any of these birds?"<br /><br />I don't know about those birds. but I found a bit about the loss of sight. We'd expect that, if the mutations behind the loss are random, then different mutations would be present in different populations. <a href="http://news.nationalgeographic.com/news/2008/01/080108-cave-fish.html" rel="nofollow">Guess what?</a>Gabohttps://www.blogger.com/profile/17552375541700079254noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-45863975007808799742017-03-27T14:34:10.420-04:002017-03-27T14:34:10.420-04:00I think we've been wasting time with txpiper. ...I think we've been wasting time with txpiper. She or he keeps repeating arguments. I think that he or she prefers to ignore corrections than understand them. I quit.Gabohttps://www.blogger.com/profile/17552375541700079254noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-8978085069125300732017-03-27T14:28:04.866-04:002017-03-27T14:28:04.866-04:00BWilson
"There are so many different mutation...BWilson<br />"There are so many different mutations that contribute to the loss of sight or the loss of flight, that it is also entirely reasonable to expect that new ones would also turn up after the animal enters conditions where sight or flight is no longer beneficial. <br /><br />Evolution of LOSS of a complex trait is not all that difficult."<br /><br />Can you identify the mutations that caused the loss of flight in any of these birds?Bill Colehttps://www.blogger.com/profile/06642212549806694659noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-74753466201281252562017-03-27T09:27:58.468-04:002017-03-27T09:27:58.468-04:00I don’t oppose those things. What I would question...<i>I don’t oppose those things. What I would question is the randomness of the mechanism that causes those things. Similar cave environment adaptations occur in all kinds of animals. I don’t think it is reasonable to conclude that they occur because of random mutations and natural selection. It looks like a planned response.</i><br /><br />Since we can point to the specific mutations that are selected against in environments where sight is an advantage in surviving and reproducing, but are no longer selected against where sight is not an advantage, what external planning is needed? If the city puts in new underground water pipes and the old unused ones corrode and waste away, do we need a planning commission in charge of corrosion?judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-59061616195826059062017-03-27T09:23:40.440-04:002017-03-27T09:23:40.440-04:00What I mean is that you have to think according to...<i>What I mean is that you have to think according to the rules.</i><br /><br />Of logic and evidence, as opposed to making shit up, yeah.<br />judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10568975332166634582017-03-27T01:12:03.602-04:002017-03-27T01:12:03.602-04:00Our understanding of ratite evolution has improved...Our understanding of ratite evolution has improved in several steps. Current thinking definitely is that ancestral members of the clade could fly, as their descendants and tinamous can now. And many of them have convergently become gigantic. Too late at night to write more about that, but this blog (https://blogs.scientificamerican.com/tetrapod-zoology/ratites-in-trees-the-evolution-of-ostriches-and-kin-and-the-repeated-evolution-of-flightlessness-ratite-evolution-part-ii/) links to both previous blogs on ratite evolution and to scientific papers on the topic. Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-75906450433747776192017-03-27T00:48:22.464-04:002017-03-27T00:48:22.464-04:00TX, lets stay on topic, which is, or was, the evol...TX, lets stay on topic, which is, or was, the evolution of LOSS of a feature, e.g. sight in cave animals and ability to fly in many birds (including not only ratites but ducks, many rails, pigeons, a cormorant and a parrot, among others). <br /><br />Many, many genes can damage or destroy a complex trait. At least one and probably more alleles that cause blindness probably exist in the "standing variation" of every common animal species. Two handy examples: alleles causing blindness exist now in both humans and dogs. <br /><br />There are so many different mutations that contribute to the loss of sight or the loss of flight, that it is also entirely reasonable to expect that new ones would also turn up after the animal enters conditions where sight or flight is no longer beneficial. <br /><br />Evolution of LOSS of a complex trait is not all that difficult. Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-24163753331415247802017-03-27T00:31:55.072-04:002017-03-27T00:31:55.072-04:00"Scientists can best make an enduring name fo..."Scientists can best make an enduring name for ourselves if we can go beyond the limits of our theories. If we can provide better explanations for the phenomena we see. That's why so many papers talk about overturning the old ideas, developing new paradigms, etc., even if they have to exaggerate a lot to do so."<br /><br />This is exactly the mental path that people walk in order to believe that meteorites or deep sea vents produced your ancestral elements, dinosaur soft tissue can last for tens of millions of years, and DNA replication errors coated your teeth with enamel. It is willful, deliberate blindness. Lewontin hit it right in the pills. txpiperhttps://www.blogger.com/profile/03645156881353741058noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10799793489185637812017-03-26T20:57:58.040-04:002017-03-26T20:57:58.040-04:00bwilson295,
“I don't understand your opposing...bwilson295,<br /><br />“I don't understand your opposing multiple of losses of sight or loss of flight.”<br /><br />I don’t oppose those things. What I would question is the randomness of the mechanism that causes those things. Similar cave environment adaptations occur in all kinds of animals. I don’t think it is reasonable to conclude that they occur because of random mutations and natural selection. It looks like a planned response.<br /><br />“Standing Genetic Variation” is a proposal that tries to work around the idea that purpose is involved. I think it is absurd, but there are people who recognize the problem for the mutations/selection paradigm. I’ve posted this article before:<br /><br /><i>”The classical view of evolution holds that organisms experience spontaneous, or de novo, genetic mutations that produce various novel traits. Nature then selects for the most beneficial, and those get passed along to subsequent generations. It’s an elegant model, but it’s also extremely time-consuming and doesn’t help species that need to cope with sudden, potentially life-threatening changes in their environments.<br /><br />With standing genetic variation, by contrast, genetic mutations arise and are passed along within a given population but are normally kept silent. The physical manifestations of the mutations don’t emerge unless a population encounters stressful conditions, like being forced to live in a dark cave instead of a vibrant river.<br /><br />“De novo mutations occur after an organism arrives in its new environment. They’re slow, and they favor dominant traits,” explained Rohner. “Standing variation provides a pool of mutations that are already available in the whole population. When organisms find themselves in a new environment, the silent variations are released and nature can select the ones that help.” “</i><br />https://hms.harvard.edu/news/evolutions-fast-track-12-16-13 <br /><br />A pool of mutations. Saving up DNA replication errors for a rainy day.<br />-<br />“And obviously their ancestors used to see (or fly) because we can see remnants of the eyes (or wings) in the currently blind (or flightless) organisms.”<br /><br />In the case of the ratites, the currently accepted idea is that their flight-capable ancestors left somewhere and flew to Africa, Australia, South America, New Zealand and Madagascar, and evolved into, respectively, ostriches, emus, rheas, moas and elephant birds. (The old idea that a ratite ancestor evolved and radiated before Gondwana broke up made a lot more sense. I don’t buy that either, but they preferred that notion for very practical reasons.)<br /><br />To say that after their arrival they became flightless birds is a gross understatement. They are all completely different from flighted birds, but but they share some striking and similar features, like gigantism. All of them make very interesting reading, but I don’t think ‘convergent evolution’ is anywhere near an adequate explanation. In my view, it is just a cop-out.txpiperhttps://www.blogger.com/profile/03645156881353741058noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-62668839971430858652017-03-26T17:19:26.380-04:002017-03-26T17:19:26.380-04:00how donors DNA and recipient DNA can form a functi... how donors DNA and recipient DNA can form a functioning unit"<br /><br />If parts of some incorporated DNA happen to look enough like a promoter, or enough like a transcription factor binding site, then they might act like one and thus "rewire" gene expression. Promoters and transcription binding sites tend to be short and variable. Thus, the probability for some random piece of DNA to look and act like one is somewhat high.<br /><br />Some friends of mine <a href="https://www.ncbi.nlm.nih.gov/pubmed/26056565" rel="nofollow">found</a>, for example, that it's likely that some low GC DNA pieces fail to be cloned into <i>E coli</i>, because their low GC content results in lots of spurious transcription (lots of pieces in those sequences look like <i>E coli</i>'s promoters).Gabohttps://www.blogger.com/profile/17552375541700079254noreply@blogger.com