Confidence in evolutionary science

Why did you bother to type that? For whose benefit did you think you were typing it for?Solipsism: keep it to yourself.

Ahem, seems like a good shoe-in for resurrecting some of the words I put into stasis last night/this morning.

Common Ancestry

Here are eight living things:RED KANGAROO
HUMAN
CHIMPANZEE
MISSISSIPPI ALLIGATOR
PLACENTAL MOUSE
MARSUPIAL MOUSE
SONG THRUSH
VAMPIRE BATSo let's try and think of some characteristics that some or all of them have. Motile might be a good one. All of them are motile (they can move), this is a characteristic that is shared by all of them. All of them are heterotrophic (they need to eat to sustain themselves). So we have shared characteristics there common to all of them. Any member of this group we'll call, for simplicity: "Animals".It also happens to be true that at some point during their life cycle, they have a notochord. So they are all "Animals", and they are all "Chordates". So far so uninteresting.What about Mammary glands? Well the Kangaroo has mammary glands, so too do humans, chimps, both the mice types, and the Vampire Bat. The others don't. So we'll call the ones that have mammary glands "Mammals". Of the mammals, only two of them have a pouch - the marsupial mouse and the kangaroo. We'll call them Marsupials, the others we'll call "Placentals" because the Placenta makes a significant contribution to nutrition which it doesn't in the "Marsupials".Finally, two of the Placentals have grasping 'hands', with flat nails (as opposed to claws). We'll call them "Primates", that includes humans and chimps.We can keep naming characteristics and assigning groupings for as long as we like. There is a problem though. All Mammals have mammary glands, but all birds have wings. What about a creature that has mammary glands and wings? Like a bat.Of course, our characteristics are somewhat arbitrarily picked, it is difficult to know what characteristics are important and what is not, but we still need a way of objectively resolving these character conflicts. One method - which should be an obviously good start is to list all the shared characteristics of bats and other mammals and likewise with birds. Whichever group has most in common with bats, is where we should place it. In this case, mammals win by a mile. This method (which I have simplified), called Maximum Parsimony, is far from perfect.Here is a tree we might compose based of physical characteristics: Now - being able to come up with a single, or a small selection of family trees based of physical characteristics and some objective collision resolution methods is something we might expect if evolution was in fact, true. Under certain conditions, if evolution were true, it must be the case that we could do this. Those conditions are true in this world, but if there were only a few life forms, closely related, it might be very difficult to create such a tree (would you expect to be able to create a family tree of your own extended family, based only on what the family member look(s/ed) like at age 25?). Other conditions may cause problems for this, but for the most part - they don't apply fully so we can, within certain error margins (that are often calculable), generate these trees.When we have eight members, there are 135,135 possible trees. (The calculation for that is 1 x 3 x 5 x 7 x 9 x 11 x 13, deriving that calculation is left as an exercise for the student). Some of those trees might look a little like each other, but most of them would be very different indeed.So let's find a way to create a tree of these animals using a completely different method. There is a protein, cytochrome b which "is one of the cytochromes involved in the electron transport in the respiratory chain of mitochondria." It is a protein that has no impact on the way an animal looks. This means that that comparing the cytochrome b genes of the animals above and creating a tree that way is a completely independent method of building a tree. If we are generous, there is a 1 in a 1,000 chance that if the animals were unrelated it would create a tree similar to the one I created above. As I said, there are 135,135 possible trees and most of them are radically different.Well, I just pulled the genes off pubmed and tested it for myself, here is a Dendogram tree I created using ClustalW. All that sounds complicated, at this time we'll just say that there are certain methods of computing trees based on differences in the way proteins are put together, some can quickly be done online for free by amateurs. That seems pretty close to me. Evolutionary prediction had a 999 in 1,000 chance of getting it badly wrong, but it didn't. That gives me 99.9% (approximate, naturally) confidence that evolution successfully predicted this tree and it was not due to just chance.OF course, we can do this for other genes, for larger sets of animals. I will skip to the chase: we get similar results. What are the chances? Astronomical. The only reason for these two completely different methods to come up with trees that are even remotely similar (and they are rarely exactly the same, due to known problems in the various methods used) is if the animals share a common ancestor and have been slowly diverging, their genes mutating, and their traits changing by descent with modification.The only other explanation that is in any way consistent is that they have been specifically designed this way in order to deliberately confuse geneticists.The theistic position on its own could never have derived this - once we invoke the miraculous power of a supernatural agent, the unit of inheritance doesn't even have to be material, it could be itself supernatural. There was no reason that there had to be genes, but even Darwin was able to see that if his theory was to work, something like genes would have to exist.Here, just to show you, is the tree I generated when I entered random characters instead of the actual gene sequences I found: That is just one of the many trees that could have been built, that would have essentially served as a strong falsification of the concept of common ancestry. Common ancestry of all life is almost certainly true based on the evidence and "perceived facts". Above listed are two independent and converging lines of evidence that both point in the same direction. The primary literature has thousands of similar tests from independent genes using different methods all coming up with very similar looking trees. Is that enough of a drawn conclusion for you?

Benefit? For the benefit of those who are looking at the issue in a broader context. I wanted to know in particluar how confidence in evolution jives with the raised questions. I am not a solipsist, but i am not afraid to confront questions. By "unreal" i meant unreal in a sense that everything is a product of pure chance, inlc. evolution.I have no idea why you get hurt over this. Would a creator being(s) that made everything look like it was random, incl evolution make me a solipsist. Was Einstein a solipsist?

The nature of reality is not the topic of this thread, which presupposes the standard definition of science and accepts reality as a given.Please propose a new topic for what you want to discuss over at [forum=-25].

---

--	Percy
	EvC Forum Director

Please do not post to this thread again. Thank you.

2nd attempt...Modulous, I was wondering if you could render me a tree (based on Cytochrome C if possible) if I give you a number of organisms? Or is this quite a bit of effort (don't bother if it would take too much of your time)?I need one of those neat graphs for an educational post I'm going to do on another forum. Edited by Annafan, : No reason given.Edited by Annafan, : No reason given.

You were asked not to post to this thread. There was time for you to read that request.You are suspended for 24 hours.

It would take time, but I don't mind doing it that much if you don't mind waiting. I recommend you learn how to do it yourself since it is shockingly easy.See Message 138 or Sequence comparisons (Bioinformatics?) or my post on everything2. The hardest part is tracking down the proteins, everything else can be simplified to copy/paste press a button (you can tweak things a little).Using http://align.genome.jp/ there is a drop down menu after you've run the analysis that will create a tree for you - and there are other stand alone programs that will do a more complete job for you with a little know how. Hope that helps.Edited by Modulous, : No reason given.

Hey, thanks. I think I found another way to get where I want to be, though. I based myself on one of those high-level Trees of Life pics that are available (like here, and that is actually enough for my purposes. But I might check out your tips as well!

Hi AdminNosy,I think you might have mistaken the post from Annafan to be from Aqobot, so I'm going to reverse the suspension. You can reinstate it if I haven't sized this up correctly.

---

--	Percy
	EvC Forum Director

Thanks for the input, and improved diagrams RAZD. I've added another section in my reply to Bertot, hopefully that helps with the curiosity. This gives me a good excuse to post another couple of smaller sections I deleted.Expert opinionThen again, maybe I'm in no position to judge this. Who better than the relevant experts in the fields in question? I can be sure they have studied the subject for a long time, read more primary literature than I, and I know there isn't a great deal of money in the field so I think I can trust them not to be in it for the money. Well over 99.9% agree that the facts of the matter (common ancestry, evolution) have been settled and that the rest is just filling out the details and explaining exactly how it all happened (honing the theory).This consistent expert opinion gives me increased confidence.And once again we turn to converging lines. Disparate fields such as geology, cosmology, archaeology, agriculture, medicine etc., are all consistent with natural history, evolution, common ancestry and so on with very little in the way of dissent from this opinion.The only argument against this kind of thinking is that there is some vast conspiracy. This is always the case when someone has a pet idea that simply doesn't line up with, or is flat contradicted by such an overwhelming body of evidence...everybody is in on a conspiracy. Maybe its an atheist conspiracy, perhaps it is a materialist one. It doesn't matter that while scientists may on the whole be biased towards certain political or philosophical preferences, there are still thousands of scientists who swing the opposite way. How a conspiracy with so many people who disagree on religion, politics, morality etc, can keep itself together is conveniently left unexplained.The arguments against evolution and common ancestryAre almost universally obviously wrong, the identification of the errors involved require a few months of proper study into the subject. They are the equivalent of someone arguing that the The Epistle of St. Paul the Apostle to the Romans was written by the Romans who were pagan which disproves God. The vast majority are just plain bad. There are quite a few that do sound reasonable, but they rely on strawmen of evolution or playing on fears...this is a problem of education and can easily be rectified. A small minority sound like killer arguments and are really hard to either see why they are wrong, or it is difficult to explain in straightforward terms the error being made.Very very often, the arguments are raised by those with a religious agenda, or those that don't like the implications of not being specially created for some reason.If evolution were wrong, after 150 years I'd expect at least some intelligent people with integrity to have criticised it in a way that wasn't ludicrous, childish, silly, based on understandable but pervasive misconceptions/straw men etc etc. Maybe they have. To date, none has been presented to me. This also boosts my confidence in the claims in question (though only in an ancillary fashion).

I misread the time on agobots last message. My apologies to him, thanks for correcting it.

Modulous, i don't want to sound like a stupid worshiper but i really wish i could have sent posts in your fashion to those with whom i was debating lately on another forum. Well, i don't see why i shouldn't mention it: the Magle International Music Forum. It's the one forum where i realized how strong the creationist position could be. I'm not saying this in terms of arguments or power of conviction but in terms of stamina and incredible "mauvaise foi" ("bad faith" in french).Rethoric is the only real tool they (creationists) can use until their opponent gives up when he's not tenacious enough. I've been tenacious and really willing not to change their minds (i always have the Zappa quote in mind*) but to try to swap points of view, in order to have some reflection, knowing that scientific research is by essence not over, and might never be, and thus being able to go beyond this indestructible wall separating faith-based conviction and will to go further in knowledge. I've not been tenacious enough, and found myself copy/pasting lots of things found after more or less long net and library research, that were hardly read. The worst feeling i got was when one of my opponents suggested that i get some degree in scientific fields (astrophysics, biology, paleontology, you name it). I mean, it was a legitimate suggestion since i virtually know nothing. So, this guy sounds very informed and all. But everything he said was cleverly made for supporting the intelligent design view only. A rethorical champion. Sometimes i wondered how i could realize that he was using hypocrisy when he at first seemed to be honest while displaying his knowledge about this or that. Well, each time i gave an answer that was fully satisfying, wether it was about exctinct species, types of mutations or anything , he just gripped to his holy book, eventually. So a quite scholar man can also be a very obtuse man, and now i've stopped posting, because i understood the goal was not to have the last word or to change anything, but to try to practice honesty in a real reflection. As you might have noticed, there rarely is such a value displayed by creationists, and that's what makes me sad.Anyway i still hope on EvC it's less rare.*Frank Zappa: "One of my favorite philosophical tenets is that people will agree with you only if they already agree with you. You do not change people's minds."Edited by olivortex, : No reason given.

Hi olivortex,
Allow me to welcome you to the site. Thank you for your kind words. If I am viewed as a poster to be envied by some, it is only so because of years of practice There are two types of creationist, those that listen and those that don't, and you'll have to be prepared to deal with a lot of the latter and few of the former whatever forum you find yourself on though I like to think that, with a strong selection pressure here at EvC we've managed to preserve some of the better samples of their species!I had a look at the forum, I saw an extremely ludicrous argument being advanced by "Robert Newman" where he argues that evolutionary scientists get confused between breeds and species in the same post as he gets confused between 'genus' and 'species'.
It's quite sad really, to see such arguments advanced with such bluster and confidence from people who clearly don't realize how little they know.

Thank you for welcoming me and thank you also for taking the time to visit the aforementioned forum. My nick is Sunwaiter. Robert Newman has been quite polite and respectful towards me but i have to admit the title of the thread itself (of which he is the originator) doesn't seem to invite any discussion, so it was partly my fault if i got into useless and circular chat. Moreover, i gave in to the temptation to post funny but even more useless links, thing i would not do here, having read several threads already, and having seen the spirit in wich they have been growing.