Oh please. If there are any "creationists" out there who are running scared, they need not do so. The new article [by Chris Mooney] is titled "You Share 98.7 Percent of Your DNA with This Sex-Obsessed Ape," referring, of course, to the precious bonobo, a chimp-like ape famous for its progressive sexual habits. Just by itself, the genetic similarity between us and apes such as the bonobo is supposed to be of knockdown importance.This is a common argument from the IDiots. They assume that the intelligent designer created a model primate and then tweaked it a little bit to give chimps, humans, orangutans, etc. That's why the genomes of these species are so similar.
But what else would anyone expect, whether on a model of Darwinism, intelligent design, or creationism? Apes and humans are similar in many ways, and you don't need Darwinian evolution to see this.
Unfortunately for them, there's a bit more to it than that. Their model of intelligent design also has to account for the fact that humans are more similar to chimps/bonobos than to gorillas and all three are about the same genetic distance from orangutans. This sequence data correlates with the fossil record over a period of about 10-15 million years.
If evolutionary theory (population genetics) is correct, and if David Klinhoffer and chimps/bonobos actually evolved from a common ancestor, then we should observe a correspondence between the percent similarity of Klinghoffer and chimps and the predicted number of changes due to evolution.
Let's see if it works.
The human and chimp genomes are 98.6% identical or 1.4% different. That difference amounts to 44.8 million base pairs distributed throughout the entire genome. If this difference is due to evolution then it means that 22.4 million mutations have become fixed in each lineage (humans and chimp) since they diverged about five million years ago.
Now, I suppose that this could be just an amazing coincidence. Maybe it's a fluke that the intelligent designer introduced just the right number of changes to make it look like evolution was responsible. Or maybe the IDiots have a good explanation that they haven't revealed?
Or maybe they're just IDiots who don't know what they are talking about.
372 comments :
«Oldest ‹Older 201 – 372 of 372Does the auto-correct function in word processing programs add information? Does not this auto-correct function counteract evolution and why was this process then selected for?
The auto-correct function in a word processor uses stored information to match to what you write. I didn't give you an example of match-repair system in DNA replication. I gave you an example of "information" gained (because it had been "destroyed"), and I asked you where it came from. Your analogy with a auto-correct function makes no sense. Quite simply, a random mutation did. And quite simply, your use of the term "information" is nonsense.
I was challenging you to give an example of a naturalistic process that could add information and that predates the biological evolution
Drop the "information" nonsense. You've been duped by the Discotute. Their use of IT is as good as their use of the second law of thermodynamics. I gave you an unavoidable example of a gain of "information" by a simple random mutation. This is the last time I'm going to waste my time with this line of argumentation. What you really want to know is the origin of the first genes. Well, so do I. Join the club.
Hi there potty mouth,
Intelligent people can explain themselves to others because they bother to listen to where the misunderstanding is occurring. People who are not intelligent are more prone to name calling as they find it difficult to vocalise their emotions. Poor things.
Now behave like an adult and actually listen - and don't try to second guess some Creationist point I am not trying to make.
Wiki says: "Punctuated equilibrium is a theory in evolutionary biology which proposes that most species will exhibit little net evolutionary change for most of their geological history, remaining in an extended state called stasis."
Do you agree with this definition? This is not a trick question. I just want to confirm that we are talking about the same thing. I last met Punctuated Equilibrium in the 80's so I'm testing myself as much as you. OMG why am I bothering? As if you will engage in an adult conversation. And why would I make myself vulnerable to a bully?
Andy, Pakicetus is not the ancestor of Basilosaurus, though it is a close relative. The moment their most recent common ancestor species split into two different lineagaes, they began to acquire new derived traits independently. They lived in different habitats, so most of those innovations would have been divergent (shaped by different environmental pressures). Anyway, whatever happened AFTER the split can't be used as evidence of their relatedness.
They do, however, share "at least one" unique innovation that is more likely homologous than convergent (and this is just enough!) plus more traits shared with artiodactyls but not other placentals, plus still more traits shared with other placentals (including you) but not with marsupials or monotremes, plus still more traits shared with all mammals but not other amniotes... etc.
You may refuse to believe that "a few million years" (in other words, a few hundred thousand generations) is enough for an animal's general body plan to change from that of a semi-aquatic quadruped to a fully marine swimmer, with fluke, flippers and all. What do you base your opinion on?
Andy can you help me? Why do they all insist on name-calling and bullying and trying to score points? Are they trying to cover up the fact that they are scared of debating honestly?
Does the auto-correct function in word processing programs add information? Does not this auto-correct function counteract evolution and why was this process then selected for?
Word processors auto-correct mistakes because they use a database to match you write. But I'm not talking about auto-correct functions in DNA replication, Andy. I'm talking about a point-mutation occurring at an indeterminate later date along a lineage. It's unavoidable that, if "information" was destroyed with the first mutation, then the second represents a gain of information. So from WHERE did that "information" come from, Andy?
Pedro, maybe I wasn't clear enough. I was challenging you to give an example of a naturalistic process that could add information...
See above for a naturalistic process creating "information".
and that predates the biological evolution, which I agree can add information within the available probabilistic resources.
I don't understand you point. You want to know the origin of genes? And by what process? I don't know. Join the club.
There seems to be some problem with blog posting. I'm getting my posts either not showing or getting posted somewhere else.
Andy can you help me? Why do they all insist on name-calling and bullying and trying to score points? Are they trying to cover up the fact that they are scared of debating honestly?
Nice try, "Pauline". Please show more of your true nature.
Either I lack the basic intelligence to understand you or you have not fully understood the point I was trying to make.
Now instead of insulting me why don't you engage in adult conversation and don't second guess some existing Creationist argument hidden in my question. Or are you scared to drop your ugly façade?
Firstly - I last came across punctuated equilibrium in the 80's. So just to ensure I'm not ignorant of a change in meaning let's agree on what it was.
Wiki states:
"Punctuated equilibrium (also called punctuated equilibria) is a theory in evolutionary biology which proposes that most species will exhibit little net evolutionary change for most of their geological history, remaining in an extended state called stasis."
Is that how you see it? (If not give me an alternative definition but this is what I thought it meant.)
Lutesuite are you completely unaware of what the term "I was there" means? Perhaps you aren't English and I should give you a break. It clearly doesn't mean I was actually in the presence of Gould all the way through writing his theory (now please tell me you're not that stupid?)
I'm old. I meant I was around doing Genetics when it happened: "I was there". It's called "figurative speech."
"Any event channeling energy from some form into another that results in some form of organization would be adding information by definition."
If only you wanted to understand and thus make the effort, but you could not care less, could you?
Good to hear that you don't have a degree in engineering. Your lack of understanding of the most basic thermodynamics would be an embarrassment to the profession (there's some engineers though ...)
Judmarc, slightly off topic, did you finally get the point about why Hawking do not believe the universe started in a singularity? You never responded to my last post.
More than slightly OT. I responded to the last comment of yours I saw at the other thread - did you post another? You never did indicate whether you knew what imaginary numbers were, which is key to understanding what Hawking actually said. What he quite clearly said was that he'd nicely worked out the math so there was no singularity in the imaginary direction, but there was in the real universe. Get the distinction? Or to ask the same question in a different way, do you know what imaginary numbers are and what they are used for in the sort of physics Hawking is doing?
I see Pauline has flounced
I'm sure "she" will be back in one of "her" alter egos.
I'm leaning toward Quest myself.
By the way "Pauline", how long are your arms ?
Poor deluded lutesuite. So intent is he to spot Creationist lies and unearth conspiracies that common sense eludes him.
Use your well-thumbed dictionary to look up "figurative speech" and when it's used.
Please tell me you're not stupid enough to think I was telling you that I was literally sitting next to Gould as he was writing his theory? Maybe I should give you the benefit of the doubt if you are American as we don't share the subtleties of English.
"I was there" means I am old - I was knocking around (figurative speech not having sex - just in case your doing it again) studying Genetics in the 1980's. I'm assuming you are younger than me.
Now take a chill pill and try to remove your façade and have an adult conversation with me without resorting to childish name-calling or bullying tactics.
So one possibility is that I truly lack the basic intelligence to understand the point you're making. It's possible. But maybe you haven't understood what I was saying. Also possible.
So just to check we are on the same page, Wiki states:
"Punctuated equilibrium (also called punctuated equilibria) is a theory in evolutionary biology which proposes that most species will exhibit little net evolutionary change for most of their geological history, remaining in an extended state called stasis"
That's what I understand by it - are we on the same page? (figuratively and literally this time :-)
lutesuite look up "figurative speech" in your well-thumbed dictionary.
Surely you're not stupid enough to have taken me literally?
"I was there" means I am so old I was knocking about (not literally having sex) studying science in the 70's.
??
??
Pauline,
I know what punctuated equilibrium means. I am not debating what it means. I am explaining to you that it was proposed after looking at some specific set of fossils that showed interesting evolutionary trajectories of particular groups of organisms. That lead to further investigation and the proposal that such might be the way in which the "tempo" of evolution goes. Long periods of stasis, then bursts of speciation.
So, going from data on well preserved organisms allows for an observation and thus the proposal of some way in which some kind of phenomena happens. A far cry from being proposed "to keep belief in evolution." Do you get it now you IDiot?
And please. It was you who insulted me first. It was you who insulted scientific work by misrepresenting the history and the work of some serious scientists and called it an excuse to keep a belief. So take a look at the mirror before telling me how immature I am. Then show some maturity by actually trying to understand the point and stop your parade of creationist stupidity.
OK Conditional clauses101
Protasis (dependent clause): "If the world was only 6000 years old,
Apodosis (main clause:) "then there would not have been enough time for the observed diversity of life to have arisen thru evolution."
When you said: "If God had created humans specially, with perfect genomes devoid of any junk, then the mutation rates she cites cannot be explained."
You included your assumption about HOW God created humans (devoid of any junk DNA) in your dependent clause.
The word "if" and the fact that this sentence is conditional is a red herring.
Call me stupid because I've only just twigged that you are calling me Pauline in inverted commas. I didn't notice as I'm not used to blogs so I didn't think that was significant. Are you being rude because you think I'm some guy called "Quest" ?? That makes a lot of sense of some other rubbish you wrote earlier. If it will make a difference to your attitude and stop your bullying then how can I prove to you that I am genuine in my desire to learn?
To see those comments click "Load more..." at the bottom of the page
"Random mutations can't add information!" is very much a Creationist argument, so anybody who presents that argument as if it were evidence against evolution has no right to complain when other people treat them like they were a Creationist. That said, there is a simple way in which any person who makes the random-mutations-don't-create-information argument, can demonstrate that they aren't just yet another goddamn Creationist spewing yet another bogus Creationist non-argument: Measure the information content of arbitrary nucleotide sequences. Because if you can't measure the information content of arbitrary nucleotide sequences, on what grounds can you assert that 'information' cannot be created by 'random mutations'? If you can't measure the information content of arbitrary nucleotide sequences, how the heck can you tell whether or not Nucleotide Sequence X has more, or less, 'information' in it than does Nucleotide Sequence X-plus-a-mutation?
So.
Here's a chance for Pauline to demonstrate that she actually does know what she's talking about, and that she's not just parroting anti-evolution non-arguments she's gleaned from whatever Creationist source: I'm going to provide two arbitrary nucleotide sequences. Pauline, please utilize any definition of 'information' you like, and any information-measuring methodology you like, to determine how much 'information' each one has—and be sure to show your work. Here's the pair of nucleotide sequences I said I'd provide:
Sequence 1: cag tgt ctt ggg ttc tcg cct gac tac gag acg cgt ttg tct tta cag gtc ctc ggc cag cac ctt aga caa gca ccc ggg acg cac ctt tca gtg ggc act cat aat ggc gga gta cca agg agg cac ggt cca ttg ttt tcg ggc cgg cat tgc tca tct ctt gag att tcc ata ctt
Sequence 2: tgg agt tct aag aca gta caa ctc tgc gac cgt gct ggg gta gcc act tct ggc cta atc tac gtt aca gaa aat ttg agg ttg cgc ggt gtc ctc gtt agg cac aca cgg gtg gaa tgg ggg tct ctt acc aaa ggg ctg ccg tat cag gta cga cgt agg tat tgc cgt gat aga ctg
Which of these two nucleotide sequences has more 'information', Pauline? Oh, and don't forget to show your work. Thanks in advance!
Andy, look up all the terms I gave you. They refer to the shared features.
Judmarc, don't embarrass yourself, imaginary numbers is introduced in high school maths. My last comment was about you conflating the singularity with Big Bang. You're now continuing on that note and conflate "imaginary time" with "not real"...
Andy
Define information.
NE first wrote:
"Any event channeling energy from some form into another that produces energy with some resulting organization would be adding information by definition."
When I told him that it was a nonsense statement he re-posted but with a sneaky editing of the claim, see below:
"Any event channeling energy from some form into another that results in some form of organization would be adding information by definition."
Well, I have another editing that can be made an then we can agree on it:
"Any event not governed by physical law that results in some form of organization would be adding information by definition."
Pauline, on your note above. Name calling is cheap, I mostly just ignore those posts same with bullying, but I guess I have to admit that I enjoy the part of trying to score points. Same as if you involved in a game of boxing you must not take the blows personally and instead use them to improve your game. I'm glad you decided to stay a bit longer, the conformity here was getting a bit boring.
I see that Andy Wilberforce is also kind of dubious regarding the ability of
'random mutations' to create 'information', so if Andy wants to take a shot at determining which of my two nucleotide sequences contain more 'information', that would be fine by me. All I ask is that you show your work, Andy, okay?
Andy, what's "sneaky" about NE's re-edited version? He didn't change anything important; he merely deleted a superfluous repetition. Your version, on the other hand, is utterly nonsensical. What events can be regarded as "not governed by physical law"?
I suppose Stephen Hawking best knows what he means and is the most reliable commentator on his own ideas (emphasis added):
If space and imaginary time are indeed like the surface of the Earth, there wouldn't be any singularities in the imaginary time direction, at which the laws of physics would break down. And there wouldn't be any boundaries, to the imaginary time space-time, just as there aren't any boundaries to the surface of the Earth. This absence of boundaries means that the laws of physics would determine the state of the universe uniquely, in imaginary time. But if one knows the state of the universe in imaginary time, one can calculate the state of the universe in real time. One would still expect some sort of Big Bang singularity in real time. So real time would still have a beginning. But one wouldn't have to appeal to something outside the universe, to determine how the universe began. Instead, the way the universe started out at the Big Bang would be determined by the state of the universe in imaginary time. Thus, the universe would be a completely self-contained system. It would not be determined by anything outside the physical universe, that we observe.
(see also the last paragraph of that small lecture, in which Hawking says the very same things Judmarc has been trying to get across to you).
I've already replied twice to Andy yesterday but my posts keep disappearing. What's going on? I'll try again.
Does the auto-correct function in word processing programs add information? Does not this auto-correct function counteract evolution and why was this process then selected for?
Autocorrection in a word processor uses a database for comparison. Your analogy is incorrect, because I'm not talking about DNA repair using a template strand for correction. The "information" was *destroyed* by a point mutation and nothing stops a point mutation from occuring again, therofore unavoidably *creating* "information". So where did that "information" come from"?
Pedro, maybe I wasn't clear enough. I was challenging you to give an example of a naturalistic process that could add information and that predates the biological evolution, which I agree can add information within the available probabilistic resources.
I don't know, and no one does, how the first genes formed. As for the origin of the "information", I would have to know what the process is. Quite clearly, as in the example above, "information" as you (ill)define it doesn't require exoteric, mystical origins. As you know, the signal from a pulsar also carries "information". Where does the "information" in a pulsar's signal comes from? Or the "information" in a molecular cloud's spectra? Or the "information" in any kind of signal that can be analyzed using Information Theory, like DNA?
You've been duped by the Discotute into buying this ill defined, esoteric view of what information is as worked on by information theorists. There's as much science in IDs notions of "information" as there is in their use of the Second Law of Thermodynamics or in the abuses of Gödel's incompleteness theorems.
Piotr, just like Judmarc you truncate the quote where it is getting interesting is it a coincidence? A few sentences later Stephen says : "The no boundary proposal, predicts that the universe would start at a single point, like the North Pole of the Earth. But this point wouldn't be a singularity, like the Big Bang. Instead, it would be an ordinary point of space and time, like the North Pole is an ordinary point on the Earth, or so I'm told. I have not been there myself."
Judmarc, you are conflating singularity with the Big Bang. General Relativity predicts a singularity at the beginning of the universe as shown in the Penrose-Hawking singularity theorems. General Relativity does however not account for the uncertainty principle and is therefore ill suited to study situations approaching a singularity. Quantum mechanics is a better theory in these situations, but unfortunately we do not yet have a quantum theory for gravitation. Also when you approach a singularity in real time the uncertainty principle which is an intrinsic part of quantum mechanics would be violated if it had not been that quantum mechanics postulates the existence of imaginary space-time. This should not be conflated with imaginary as in "not real". This means that if there were a theory of Quantum Gravity, this could be used to described the initial state of the universe without the laws of physics breaking down when applying the no boundary proposal.
Now we must not conflate this theory with the cause of the existence of the universe. This is how Hawking expresses it: "What is it that breathes fire into the equations, and makes a universe for them to govern. Is the ultimate unified theory so compelling, that it brings about its own existence? Although Science may solve the problem of ~how the universe began, it can not answer the question: why does the universe bother to exist? Maybe only God can answer that."
Pedro,
To see your comments click on "Load more ..." at the bottom of the page.
Andy shows once again that he could not care less about answers. He will look like an idiot if necessary (claiming that producing information does not follow physical laws!), but will not try and understand explanations. Then they are surprised that we call them IDiots.
Andy, you aren't pulling your credentials on me because you seem to know that you don't have any that are relevant. But you did pull Pauline's credentials, and you mentioned those of others (though not of any of the biologists posting here, oddly) in order to belittle them.
Of course it's really the quality of the arguments that matter. You and Pauline lose there too, though.
I don't seem to have a "load more" option at the bottom of the page...
But it seems it's working now anyway, so thanks. Sorry Andy for the triplicate posts.
I clicked here because I can't reply where I want to.
Firstly, you accused me of being rude to you first. If you feel that way I sincerely apologise, but I had received a tirade of abuse and pleaded several times for people to be polite. I can understand if you thought I was someone elase (Quest?) (I still don't know why someone would pretend to be someone else as no-one replied to that particular question of mine) but if you thought that, then maybe I understand why you got annoyed. However, I was utterly shocked at the response I received and incredibly hurt so I lashed back. But you are right I shouldn't have been rude and I apologise.
I asked you if you agreed with the Wiki definition of punctuated equilibrium.
I know you're suspicious but honestly the only reason I asked was in case we were talking at cross purposes. So the way I understand it is that the fossil evidence pointed to long periods of stasis and relatively "short" (in evolutionary terms) bursts of change / speciation.
My understanding is that evolution theory would predict phyletic gradualism, so this discovery was an observation contrary to what was expected. So why was it called a theory? When I said "I was there" (and I meant it figuratively) I meant there was a lot of discussion at that time about hypothetical processes that could be responsible for this discontinuity (allopatric speciation was not considered to be a likely candidate for all the examples.) So punctuated equilibrium was not an evolutionary theory that predicted evidence that was confirmed in the fossil record. It was simply a description of how the data didn't fit the existing theory, so as such at the time it was evidence against evolution but was spun into a new insight into evolution. That's what I meant to say if I had been in control of my feelings. This is not an argument; I'm not trying to persuade you of anything, I'm asking if this is also what you think happened.
Another good example of I heard of recently was the discovery of red blood cells (sic) and protein in T-Rex bones. My concern here is that the researchers only followed possible explanations that fitted with evolution (contamination, unusually long preservation by an unknown method - all absolutely necessary to explore in my opinion) but they didn't consider that the bones might be younger than originally thought. In fact the researcher got extremely annoyed when Creationists suggested this. Surely a scientist following objective data and being open to every possibility would have also explored this?
I'm expecting you to say that there would be no point because evolution is undisputed fact. All I'm saying is that that is exactly the mindset of previous paradigms (earth as centre of Universe, flat earth...). These are now emotive ridiculed concepts but in their time they were undisputed facts. Scientists who believed these (now disproven) theories were not stupid, it was just the unquestionable mindset of the day.
I'm not saying that the dinosaur blood disproves evolution. Obviously it's just one bit of data, but when people on this site ridicule open-mindedness that's surely not good for science.
Having experienced the vitriolic abuse I unearthed I'm even more concerned - evolution is really a faith isn't it? I mean people are overly emotionally attached to it.
Again - I am here to learn so would appreciate your thoughts.
Larry is using correct numbers. A recent paper by Kevin Langergraber et al., in PNAS used demographic data to come up with estimates for wild chimps that range from about 25-28. And there is a great paper by Jack Fenner in American Journal of Physical Anthropology (2005) that calculates generation times for humans at 29 years.
Do you have complete citations for those? It would make life slightly easier.
I wouldn't agree with the definition of PE you gave, regardless of where it came from. Yes, stasis is a part of PE, but it's not the only part. I would say that PE is ultimately a theory about a linkage between morphological evolution and speciation: stasis most of the time, change during speciation. As such I think it's false.
No, evolutionary theory doesn't predict phyletic gradualism. Why would you think so? The discovery (if that's what you want to call it) apparently wasn't expected by paleontologists, but I think that was a result of a confusion of time scales. Darwinian evolution is gradual on a human-lifetime scale, but likely episodic on a geological time scale. If you will just read Eldredge & Gould 1972, the original paper on the subject, you will see the actual data that led them to their theory, and it wasn't an absence of data; it was fine-scaled fossil data from Phacops trilobites and Cerion snails.
If you want to suggest a 6000-year-old earth and a global flood as an alternative to the standard geological time scale, come out and say so. Otherwise, a young age for various dinosaur fossils is not compatible with stratigraphic and radiometric data. That isn't about evolution at all, but about the age of the earth.
No scientists ever believed the earth to be flat. The earth as center of the universe was never really a scientific hypothesis either, just an unquestioned assumption that was eventually dethroned by observation. Your claims here lead toward the idea that we know absolutely nothing. But that isn't true. There's a lot we know, and common descent is one of those things. Nothing is ever 100% certain, but some things are close enough that we can afford to ignore the difference. Or as Carl Sagan said, it's good to keep an open mind, but not so open that your brain falls out.
The reason people think you aren't being honest with us is that you keep bringing up common creationist claims but never anything else. You ask no questions that aren't of the form "given this creationist claim, isn't there something wrong with evolution?", which is not something one would expect from a simple seeker after truth, or from someone merely trying to update her knowledge of biology. And those are my thoughts.
Hoo boy. Now it's the collagen (no red blood cells) that were found in the dinosaur fossils. Just keep ticking off those creationist boxes, "Pauline". But you're not a creationist, oh no, not you.
Just what do you think the paleontologists should have done there? What do you think they should have done to investigate if maybe dinosaurs did co-exist with humans, after all, just like your creationist buddies say?
Another good example of I heard of recently was the discovery of red blood cells (sic) and protein in T-Rex bones. My concern here is that the researchers only followed possible explanations that fitted with evolution (contamination, unusually long preservation by an unknown method - all absolutely necessary to explore in my opinion) but they didn't consider that the bones might be younger than originally thought.
They didn't take this possibility seriously because the fossil comes from the Hell Creek Formation, which is reliably dated at 66.8-66 Mya. There's simply no earthly way the bones can be younger than that. There are of course numerous other Tyrannosaurus rex fossils, all of them Maastrichtian, without exception. All that the find demonstrates is that in some very special circumstances organic material may be tougher than previously believed. Actually, a few months ago the same researchers proposed a plausible preservative mechanism (see Mary H. Schweitzer, et al., 2014, "A role for iron and oxygen chemistry in preserving soft tissues, cells and molecules from deep time", Proceedings of the Royal Society B, published online 26 Nov 2013).
In fact the researcher got extremely annoyed when Creationists suggested this. Surely a scientist following objective data and being open to every possibility would have also explored this?
Dr. Schweitzer had every right to get annoyed when some ignorant young-Earth creationists tried to hijack her results. The kind of people who blithely "reject" radiometric dates just because they are inconsistent with the Bible surely don't attach much weight to "objective data".
By the way, the survival of dinos past the K/P boundary would not be inconsistent with theories of evolution. Evolution did not require them to die out. The mass extinction that killed off tyrannosaurs, among others, was an accident, not an evolutionary process. In fact, some dinosaurs did survive it and their descendants have diverged into about 10 thousand extant species. John Harshman can tell you more about them. The fact that they are still with us does not disprove evolution -- quite the opposite.
Yep,
Fenner JN. 2005 Cross-Cultural Estimation of the Human Generation Interval for Use in Genetics-Based Population Divergence Studies. Am J Phys Anthropol 128: 415-423
Langergraber KE et al. 2012. Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution. Proc Natl Acad Sci USA 109: 15716–15721
I find it interesting that animals with ages at sexual maturity differing by what I suppose to be a factor of about two are so similar in generation times. I had thought there would e a good correlation between those variables.
@John Harshman,
Chimps and bonobos are like humans. They don't have sex until they are married. Besides, even if they have sex while they are still teenagers they can't get pregnant, as any teenager will tell you.
John, you only need to scroll up a few comments to see how wrong you are. I did not bring up Pauline's degree Christine did when she wrote: "You're not so much engaging with a gang of "self-righteous bullies" as with real scientists whose education in science in general, and genetics in particular, far outweighs yours. A Cambridge undergraduate degree doesn't count for much if you haven't kept up in the field since obtaining it."
My point is: why would her undergraduate degree make her un-worthy of posting here? And why does it justify people with even less credentials bullying her? You and many other here pretend that you do not care about degrees and credentials but you still bring it up any chance you get. And why would you say: "Andy, you aren't pulling your credentials on me because you seem to know that you don't have any that are relevant." if you wouldn't care about it?
John wrote: "The earth as center of the universe was never really a scientific hypothesis either, just an unquestioned assumption that was eventually dethroned by observation."
Well John, you should have included some history of science in that precious degree of yours. Astronomers doubted heliocentrism due to the absence of an observed stellar parallax.
No one is belittling "Pauline" because of his/her/its undergraduate degree. She is being belittled on that topic because she flaunted that degree as if this somehow mitigated the utter ineptitude and ignorance of her every post.
Recall, here is how she brought it up:
I am an "IDiot" who is able to understand the scientific evidence in favour of evolution, I have a Natural Science degree from Cambridge University, specialising in Genetics in the 3rd year.
...as if her having an undergrad degree means we are supposed to concede that she understands the evidence in favour of evolution, when that is manifestly not the case.
Andy, you should have scrolled up just a few more comments, as lutesuite has pointed out. And your point is countering a claim that nobody has made. It isn't her undergraduate degree that's the problem; it's her frequent display of ignorance. And nobody says she's unworthy to post here; she's just consistently wrong and arrogant about it, which has invited both ridicule and gentle (mostly ignored) correction.
I and others have only mentioned credentials at all because Pauline boasted about hers. I'm glad you have the good sense not to boast about yours. If you can find anywhere I have mentioned mine where it wasn't strictly relevant, please point that out.
You have a bit of a point, in that geocentrism vs. heliocentrism was a matter tested early in the history of science. But why was geocentrism the supposed default position? After all, there are two possible reasons for the absence of detectable parallax, so why assume that the reason was geocentrism? It was simply a traditional belief based initially on a naive view of everyday observation. It lasted a lot longer than the similarly engendered idea of a flat earth because contrary evidence demanded more specialized observation. But it was never held for scientific reasons.
At any rate, the entire point is peripheral to my main message, which you have ignored: evolution isn't going to be overthrown by some other idea, no matter how often creationists mention Galileo.
John, wrote: "If you can find anywhere I have mentioned mine where it wasn't strictly relevant, please point that out."
Well, admit that I maybe overstated the case in the heat of the discussion.
@Harshman: "Of course, human and chimp protein-coding DNA are on average about 99.5% similar."
Do you have a handy reference for that?
Piotr wrote: "What events can be regarded as "not governed by physical law"?"
Random mutation is not governed by physical law as opposed to e.g. crystal formation.
What would happen if The Designer of life suddenly appeared and proved that he really his the ONE....? What would happen if HE was able to create things...? Recreate things...? Would the atheistic world believe in Him....? My bet is simple and true: "NO"
Anybody here would like to debater challenge that...???
Please enlighten me on how "random mutation" does not conform to the laws of physics and what makes it so different from crystal formation.
Pauline,
Others here have given you several and clear explanations. So I have little science to add. I will remind you that originally you did not bring punctuated equilibrium into the conversation as a challenge to gradualism. You presented it as an excuse to "keep belief in evolution"; to explain gaps in the fossil record.
Your new presentation back-pedals and forgets your original intent. Maybe you forgot. OK then. How on Earth can a proposition based on observed evolutionary events, be a challenge to the very thing they show: evolutionary events!? How can a proposition based on observed evolutionary events be "an excuse to keep belief in evolution"?
So, please, how could we be "bullying" you for your "original" ideas and challenges to a theory when you just copy these well-known-and-worn-out pieces of creationist propaganda? If you gave it some thought you would understand that it's not challenges to a scientific theory that are a problem. Real scientific questions and challenges are welcome. Bullshit, on the other hand, is treated in various ways. One of them scorn.
If the "Designer" actually appeared and proved his existence? Of course. Why wouldn't anyone believe then?
What if someone develops a time machine and we are able to directly witness the entire 4 billion year course of the evolution of life? Would creationists finally accept that it actually happened?
These are pretty stupid questions, aren't they?
Don't make me laugh, "Pauline". The last thing a creationist wants to do is learn. Ask Larry how many years he has spent attempting to teach them something about evolution, and how much success he has had. I could hardly expect to do better than he has.
No, my only hope is that you creationists will eventually shut the fuck up and enjoy your ignorance in silence, and if insults and ridicule are best way to achieve that, then so be it.
Piotr, you surprise me, you and I actually agreed on this after a long exchange starting with Rumraket's tornadoes e few months ago.
I don't recognise it as remotely like to anything I might agree on. Please quote the post in which I claim that random mutations do not conform to the laws of physics "as opposed to" crystal formation.
Piotr GąsiorowskiSunday, October 06, 2013 4:10:00 PM
Piotr, glad that we now agree that base pair sequence does not depend on physical law as a posed to crystal formation and tornados.
The laws of physics make a DNA molecule possible. It's an aperiodic polymer, and the laws of physics have nothing to say about the order in which the different nucleotides are arranged. They allow the order to be arbitrary, ahich is precisely why that particular molecule can encode information. If the order depended rigidly on the laws of physics, DNA would have no "memory". I think you may rest assured Rumraket knows that.
out of curiosity - does anyone know whether Oliver the Chimpanzee's genome will be published? I for one would be most curious what made random mutations rendered him so human-like. I am guessing HACSN1 a likely candidate.
Harshman: "human and chimp protein-coding DNA are on average about 99.5% similar."
Do you have a handy reference for that? I shall google...
Pedro wrote: "Autocorrection in a word processor uses a database for comparison. Your analogy is incorrect, because I'm not talking about DNA repair using a template strand for correction. The "information" was *destroyed* by a point mutation and nothing stops a point mutation from occuring again, therofore unavoidably *creating* "information". So where did that "information" come from"?"
I have already agreed (see above) that random mutations can add information within the probabilistic boundaries.
Pedro wrote: "Quite clearly, as in the example above, "information" as you (ill)define it doesn't require exoteric, mystical origins."
I have never made any such claim, but for reasons explained above probabilities of 10E140 and over makes me very skeptical to the alternative.
Diogenes: I don't know if you'll ever see this, because this thread seems to have exceeded its capacity for easily seen replies. But anyway, I would have thought it would also be in the chimp genome paper, but it turns out not to be. I don't offhand know where that number comes from.
No responses from either Andy or Pauline. Pity, that. Here I was hoping that somebody who raises the random-mutations-can't-create-information argument would actually be able to measure the information content of arbitrary nucleotide sequences. Ah, well. If they don't mind the fact that their silence on this point supports the conclusion that the random-mutations-can't-create-information argument is unfounded bullshit, who am I to tell them otherwise?
Andy, where in that quote do I say that random mutations do not conform to the laws of physics? In fact, I didn't even mention random mutations (which are, of course physical/chemical events well explained by physics as we know it).
Those "laws", by the way, are human formulations of the regularities of nature. They have changed in the past and will no doubt change in the future as science makes further progress (even if the regularities they try to capture may be universal and immutable). Any division of natural phenomena into those that "are governed" by the laws of physics and those that aren't (simply because our "laws" are too crude to predict everything) is artificial.
Please also note what I said later in that thread.
I have never made any such claim, but for reasons explained above probabilities of 10E140 and over makes me very skeptical to the alternative.
Cells don't form spontaneously in one step from a pool of ready-made parts. In a multistep model, you would have to know what processes (concentration by dissecation/hydration, concentration by ion gradients, vesicle formation and chemical concetration, replicating polymers, or whatever they may be) are involved. Without knowing this, there's no way you can calculate any probabilites. You already know that, of course.
As for the creating information as in my example above, getting a point mutation in a particular place at some point down a lineage in a 1KB sequence is quite easy, specially with gene duplication and no need for sequencial mutation, as well as the neutrality of most changes. So the probabilistic boundaries for adding "information to a gene are pretty high.
Of course, you can just keep repeating "10E140" in your head and hope it turns true, but you're just fooling yourself.
Andy said:
Therefore if you do it in one or 10E9 steps is irrelevant mathematically the probability is still not better than 10E40,000.
Quite wrong, for the reasons I gave above. Chemistry for idiots example:
I add neucleotides to water. Assuming no degradation, nothing much will happen. They won't polymerize. Sit all you want.
Now I add bipolar lipids to water. Within seconds I get micelles (WOW, purelly chemical organization!!!)
Should be pretty obvious, to anyone with basic high-school chemistry and probabilities knowledge, that the probability of one reaction occuring in one case is completely different from the other case. That takes us to the point above that without knowing what the conditions and reactants at any step are we CAN'T calculate probabilies. And since no one proposes a model in which cells pop into existance in a single step out of basic constituents, the probability of 10E140 or 10E40,000 or whatever you want is meaningless.
Piotr GąsiorowskiSunday, October 06, 2013 4:10:00 PM
Piotr, glad that we now agree that base pair sequence does not depend on physical law as a posed to crystal formation and tornados.
Are you sure you're not quoting yourself, Andy? I didn't see the original post, but why would Piotr start a reply to you by calling you Piotr?
Piotr, I haven't said that random mutation doesn't conform to the laws of physics, I said that they weren't governed by the laws of physics. This is an important distinction.
You go on to argue for determinism saying "Any division of natural phenomena into those that "are governed" by the laws of physics and those that aren't (simply because our "laws" are too crude to predict everything) is artificial."
Well guess what, the war is over and the determinists lost. God IS playing dice. Ask Heisenberg if you don't believe me.
Pedro wrote: “So the probabilistic boundaries for adding "information to a gene are pretty high.”
I’m not sure why you keep going on about this, we are in agreement. The original question though, was about processes pre-dating biological information that can add information. This would be required in order to reduce the estimated 10E40,000 probability of getting the first replicator.
Let’s take a very basic example, I just want to make a point about your suggestion that any process would impact the probability (which is sort of true, you can lower them) and mine that only processes adding information would be able to increase probabilities. We can illustrate with a chain of 10 coin flips, after each flip you lay down the coin. The probability of repeating that particular chain next time you try is 0,5^10, i.e. 1 against 1024. (And no, I'm not suggesting that there is only one possible chain of amino acids in a protein, the point here is not how to calculate that probability). You could REDUCE your chances by repeating the flips with a set of coins having neither “heads” nor “tails”. Then the probability would be zero. This would be equivalent to your none-reacting chemicals. The million dollar question however is: would it be possible to INCREASE your chances when repeating the flips? My argument is that it would require that you somehow “cheat” i.e. that you add information. To my knowledge there is no materialistic process pre-dating biological evolution that is able to increase the information content, but if you know of any, then please let me know.
Your other hang-up seems to be the stunning number 10E140 for the maximum number of events in the observable universe. This is still an extremely conservative estimate. The number is scientifically well established based on: the age of the universe, the number of particles in the observable universe and the absolute limit on the interaction between particles (Planck time). This is valid unless you would be able to show that any of those facts are not true, in which case you would probably be in line for the next Nobel Prize in physics.
Andy, look at the list I gave you. All those specify shared derived characteristics, that's why both species qualify as members of all those groupings.
I feel that anyone who has genuinely tried to understand Haldane's Dilemma would know that it does not even provide a limit on positive selection let alone on evolution a whole. This was established in the 60s, and Haldane himself was pretty clear about how his cost of selection applied.
In other news PZ Myers claims that abiogenesis is cop-out. I don't really know what it means but it sounds pretty bad the "beleivers" hihihi
To my knowledge there is no materialistic process pre-dating biological evolution that is able to increase the information content, but if you know of any, then please let me know.
Yes Pedro because this piece of shit named Andy can't read. So please explain to Andy again how natural processes add information to a system only to see him produce a red-herring and ignore your explanations.
Ah, so that's how Hawking expresses it? And here I thought this is how Hawking expresses it:
If space and imaginary time are indeed like the surface of the Earth, there wouldn't be any singularities in the imaginary time direction, at which the laws of physics would break down. And there wouldn't be any boundaries, to the imaginary time space-time, just as there aren't any boundaries to the surface of the Earth. This absence of boundaries means that the laws of physics would determine the state of the universe uniquely, in imaginary time. But if one knows the state of the universe in imaginary time, one can calculate the state of the universe in real time. One would still expect some sort of Big Bang singularity in real time. So real time would still have a beginning. But one wouldn't have to appeal to something outside the universe, to determine how the universe began. Instead, the way the universe started out at the Big Bang would be determined by the state of the universe in imaginary time. Thus, the universe would be a completely self-contained system. It would not be determined by anything outside the physical universe, that we observe.
First, yes, still a Big Bang singularity here in our real universe. (Can't really be argued after COBE, and Hawking wasn't inclined to argue against it before, as he and Penrose showed.) Second, not determined by anything outside the physical universe - understand the implications?
Photosynthesis, a catalyst lowers the activation energy for a reaction it does not determine the order of e.g. amino acids in a protein. To place them in a certain order to get a functional fold takes either luck or information.
Rignt, Andy. So if a rock lands on wet sand, the sand will form an image of the shape of the rock. This process is not dependent on the chemical properties of the sand nor of the rock. Yet "information" now exists in the sand: We can determine the form of the rock from its impression in the sand. Do you think this process involves supernatural magic or "intelligence"? Where?
I did not attest that punctuated equilibrium was invented with no data. I said it was proposed to maintain belief in evolution. I see that's why you were so keen to ask if I'd seen his fossils and why I thought that was a bit pervy.
This is the way I saw it: Evolution predicts gradual change. Oh dear, the data disproves this. Well this can't possibly be evidence against our sacred theory so let's amend the theory to fit the data - punctuated equilibrium! That's our new theory. Now we have to come up with a process to explain it ... um...
That's the way it went - rather than the more respectable: evolution predicts this fossil data. Let's go looking to check it out. Oh great! The data fits our theory - that's encouraging.
Pauline,
See, this is why people think you're lying when you claim not to be a creationist. Once again you present the standard creationist party line. It's nearly certain that you have never read the paper in which PE was announced: Eldredge, N., and S. J. Gould. 1972. Punctuated equilibria: an alternative to phyletic gradualism. Pages 82-115 in Models of Paleobiology (T. J. M. Schopf, ed.), which by the way you could easily find on the web. You seem to be getting all your information from creationist sources. Why?
No, PE was not intended to save evolution. No, evolution doesn't predict gradual chance in the sense you mean here, though some paleontologists once thought it did. So, do you have any idea how new species might arrive? If not evolution, what's your alternative?
Again Pauline,
The data show evolutionary trajectories. How can data that show evolutionary trajectories be a problem for evolution? How can a process describing evolutionary trajectories be an attempt to keep belief in evolution? Your claims make no sense except as being part of creationist propaganda. Why won't you read the many explanations already given?
As John explained, PE is about the tempo of evolution. It is not about whether it happens or not. How could it if these researchers were looking at fossils that contained evolutionary histories? That some people thought that evolution should be somewhat continuous means that some people mistook gradual change with change at precise rhythms. But there's nothing in evolutionary theory stating or requiring either tempos. Nothing. The theory talks about variability, environments, selection. Therefore, we can expect that if the environments do not change a lot, then maybe changes in organisms will be much less evident (stasis).
Judmarc, you still truncate your quote just when it's getting interesting and you still haven't figured out that imaginary space-time is part of the real universe...I'll pick up this thread some other time but in the mean time please try to study some basic cosmology, it really would make this discussion so much more interesting for both of us.
Hmm, Lutesuite tricky question. Where does the information that you get out of your xerox come from...hmmm, guess that I will have to sleep on this riddle.
Thanks for the Mitchell & Skinner (2003) reference. I took your advice and read it carefully. It was very detailed about dental and skull evolution but apart from the very bold:
Throughout the giraffid fossil record there is clear evidence of
progressive limb and neck elongation
There was scant reference to actual lengths of necks discovered.
I found the history demonstrated that there once was an issue but I am open to you telling me that more recent discoveries have shown otherwise.
Gould (1996): "ancestral species are relatively short-necked and the spotty evidence gives no insight into how the long necked modern species arose...The standard story is, in fact, both factuous and unsupported."
Hitching (1982): "There are no intermediate forms showing a three-quarter length giraffe neck...what little evidence there is, is consistent with Gould-Eldredge's punctuated equilibrium."
Wesson (1991) "The evolving giraffe line left no middling branches on the way, and there is nothing, living or fossil, between the moderate neck of the okapi and the greatly elongated giraffe."
This documentation of respected scientists is called "an enduring folklore tale" by Skinner and Mitchell (???)
Returning to the promising:
Throughout the giraffid fossil record there is clear evidence of
progressive limb and neck elongation
it appears that the current hypothesis is that the numerous changes necessary to support longer necks evolved first in short necked Leptomerycids (waiting around for the neck to be lengthened at a later date but these changes having no selective advantage until the long neck arrived.)
Sentences like "it is in the palaeotragines that giraffe-like limb and neck elongation seems to gain momentum" do appear disingenuous when the author has already stated that palaeotragines had neck lengths identical to modern okapis. The only reason for stating this seems that the next species - Bohlinia had neck lengths identical to modern giraffes.
I also found a reference to Nikos Solounias of the New York Institute of Technology discovering a Bohlinia fossil with "intermediate neck length" in 2009 but can find no publications, only claims that one was being studied for publication. The claims were that this discovery was significant - implying that intermediate neck lengthened giraffes were still not abundant in 2009. This sounded exciting so I wrote to the Institute for details but have had no reply yet and can't find any publication by internet search (however I'm not skilled at that so please tell me if you know of one.)
Can anyone send me evidence of intermediate length necked giraffes? I also read the Wolf Ekkehard Lonnig paper you told me of and he says he wrote to various giraffe researchers begging them to publish any evidence they had of "intermediates" between short and long necked giraffes but got no reply.
So "Pauline" wants a fossil of a species of girrafid whose neck length is intermediate between some of those that are already known to have existed. Doesn't she realize that this would only increase by one the number of intermediates who are missing?
I'm glad to hear that creationist imbeciles like Wolf Ekkehard Lonnig are being ignored by working scientists, however. I'd hate to think a moment of their valuable time was being wasted providing fodder for his ignorant religious propaganda.
@lutesuite
I do understand the frustration that Creationists give you by insisting on "intermediate" types or missing links. And I get the maths - thanks :-). (It's plural in the UK) If the giraffe fossil record had many intermediates then your cry for reason would be justified, but please! There are NO fossils of neck length intermediate between modern Okapi and modern giraffe. This is a CHASM.
Asking for just one intermediate is not unreasonable. What is unreasonable is asking for 2 then 3 then 4 etc as the data is revealed. I understand you are scared but please have more trust in evolution if that is what you believe in and show me just one intermediate length fossil?
I am not saying the lack of an intermediate is proof of Creation. I am only asking for a logical, objective viewpoint. What I am seeing is a "faith" position with scientists overplaying evidence for evolution. No, I don't have a better explanation, but does that mean that we should fabricate the robustness of the evidence for evolution?
Oh, Pauline, Pauline. Fossils are not the main evidence for evolution. That would be molecules. Giraffes are just one little family within the order Artiodactyla, which also includes cows, camels, pigs, hippos, and whales. The evidence for all of this is ironclad.
Now, if you ask me (though this is pretty much irrelevant in the face of the molecular data), okapis are in fact giraffes of intermediate neck length, since they have quite long necks and legs compared to the typical artiodactyl. If we had living giraffids half way between okapis and giraffes, you would be asking for something three fourths of the way. Face it: you're Zeno's creationist.
This article peaks my interest, because I plan to work with Bonobos in a few years. Interspecies communication as well as educate non human primates in writing.
I'm also very interested in consciousness (which I hope to study as well with non human primates)
Well, want to run this idea to those reading:
Consciousness evolved in a fashion similar this?
Physical sensation capability——bacteria/viruses/fungi then plants
Conscious Awareness of physical sensation and memory of the physical sensation- invertebrates, some vertebrates like worms, mollusks, fish, bugs, amphibians, reptiles (they all have chemicals required to feel physical pain)
Conscious emotional awareness of physical sensation- vertebrates like birds and mammals (developed now an emotional responses and emotional attachment to pain of the physical as well I think -so loss of their physical offspring for example creates an emotional response)
Conscious mental and emotional awareness of physical sensation- some vertebrates -primates (now developed a mental response or mental attachment to the pain -qualifying it into intellectual terms, they have thoughts about that emotional pain attachment and that physical sensation)
Bonobos are amazing. This article is very interesting since I want to work with Bonobos.
But first, I want to run some ideas of consciousness and how it evolved:
Physical sensation capability——bacteria/viruses/fungi then plants
Conscious Awareness of physical sensation and memory of the physical sensation- invertebrates, some vertebrates like worms, mollusks, fish, bugs, amphibians, reptiles (they all have chemicals required to feel pain or better to say the physical pain)
Conscious emotional awareness of physical sensation- vertebrates like birds and mammals (developed now an emotional responses and emotional attachment to pain of the physical as well I think -so loss of their physical offspring for example creates an emotional response)
Conscious mental and emotional awareness of physical sensation- some vertebrates -primates (now developed a mental response or mental attachment to the pain -qualifying it into intellectual terms, they have thoughts about that emotional pain attachment and that physical sensation)
Actual neck lengths vary a lot even within a single genus -- see Palaeotragus, pace Pauline's assertion that all palaeotragines were okapi-like. Giraffe paleontologists say very clearly that while Hitching's claim was justifiable in the 1980s, it wouldn't be so today. Pauline... well, Pauline disagrees. A gap filled is two new gaps produced. Yaaawwwn.
"Zeno's creationist". LOL! Pure gold.
@Piotr
Pauline... well, Pauline disagrees
Once again you are assuming that because I am asking questions that I have a particular (usually Creationist) view. I have never "disagreed" I have clearly asked if there is evidence of neck length intermediate between Okapi and Giraffe. I'm asking for evidence, I'm not saying that I don't believe it happened. The evidence given for teeth is interesting - where is the neck data?
Yes I understand that giving one intermediate can lead to a slippery slope, but surely you must think it unusual that we don't have a whole range of intermediates even with PE these changes can't have happened overnight.
So could you please give me real data rather than the horribly vague:
Actual neck lengths vary a lot even within a single genus -- see Palaeotragus
Define "a lot". Are there steps all the way or are these neck lengths within normal population variation for extant Okapi and Giraffe.
The reason I want to know about Giraffes is because in the UK Evolution is to be taught to 6 year olds for the first time. I think this is great. I'll just repeat that because you'll think it's a misprint. I think this is great. Evolution is the best scientific theory we have today to explain life's diversity. But they have taken the "lengthening" of the giraffe's neck as the best example for evolution. Surely there are better examples! This also worries me because some teachers will be teaching Lamarkism.
I also think that kids should be allowed to question and shout "the Emperor has no clothes!" but with the censure of evidence against Evolution, curiosity is repressed and I think we need to encourage scientific questioning in our classrooms.
@lutsuite
Rignt, Andy. So if a rock lands on wet sand, the sand will form an image of the shape of the rock. This process is not dependent on the chemical properties of the sand nor of the rock. Yet "information" now exists in the sand: We can determine the form of the rock from its impression in the sand. Do you think this process involves supernatural magic or "intelligence"? Where??
Wot?
The information (shape) exists in the rock. The impression in the sand IS information but it is the same information as in the rock, so the amount of information has not increased.
Was it you who sent me 2 sequences of bases and challenged me to say which had more info? I want to answer that but the question has disappeared.
"Censure of evidence against evolution?" And what evidence might that be, "Pauline" who isn't a creationist?
The point, "Pauline", is that this information, which you admit exists and which has now been transferred to the sand, does not require the input of an intelligent being. So why would "information" require "intelligence" when it exists in the form of physical arrangements of nucleotides, rather than in physical arrangements of rock or sand?
It wasn't me who asked that question, it was Cubist. But it's great that you're going to answer it. Here it is, copied for your convenience:
Here's a chance for Pauline to demonstrate that she actually does know what she's talking about, and that she's not just parroting anti-evolution non-arguments she's gleaned from whatever Creationist source: I'm going to provide two arbitrary nucleotide sequences. Pauline, please utilize any definition of 'information' you like, and any information-measuring methodology you like, to determine how much 'information' each one has—and be sure to show your work. Here's the pair of nucleotide sequences I said I'd provide:
Sequence 1: cag tgt ctt ggg ttc tcg cct gac tac gag acg cgt ttg tct tta cag gtc ctc ggc cag cac ctt aga caa gca ccc ggg acg cac ctt tca gtg ggc act cat aat ggc gga gta cca agg agg cac ggt cca ttg ttt tcg ggc cgg cat tgc tca tct ctt gag att tcc ata ctt
Sequence 2: tgg agt tct aag aca gta caa ctc tgc gac cgt gct ggg gta gcc act tct ggc cta atc tac gtt aca gaa aat ttg agg ttg cgc ggt gtc ctc gtt agg cac aca cgg gtg gaa tgg ggg tct ctt acc aaa ggg ctg ccg tat cag gta cga cgt agg tat tgc cgt gat aga ctg
Which of these two nucleotide sequences has more 'information', Pauline? Oh, and don't forget to show your work. Thanks in advance!
I don't know why I bother:
Pauline:
The information (shape) exists in the rock. The impression in the sand IS information but it is the same information as in the rock, so the amount of information has not increased.
I already explained your mistake in this regard before. Here: the information in the print is not exactly the same as in the rock, and it is still more information overall because the print is information about the rock, not the rock itself. If you want to grasp why imagine having to describe the rock itself. It would take some number of bits. To describe the print in the sand you necessarily have to add things to the rock's description. The necessary extra descriptions to get both the rock and the print is more information by definition Pauline. Do you get it, or you rather really don't care?
@lutesuite
"Censure of evidence against Evolution" You are kidding aren't you? People have been sacked for questioning evolution. Have you seen the film "Expelled"? Just a few days ago we have:
http://www.uncommondescent.com/intelligent-design/a-world-famous-chemist-tells-the-truth-theres-no-scientist-alive-today-who-understands-macroevolution/
@lutesuite
"Do you get it, or you rather really don't care?" (sic)
Why am I given this dichotomy? These are not logical opposites. I DO care and I am clearly not "getting" whatever it is you are trying to tell me. It's not through wilful dishonesty (as I'm sure you are assuming as you persist on your inverted commas) so please do continue to "bother" as I'd really like to understand information theory so I am grateful to you. However, I don't think the topic is as facile as you make out.
The stone and sand analogy is interesting.
Shannon's theory assumes that if the information is already known (the shape of the stone) then actually NO information has been transmitted in your example.
I'm also interested in your view about two other aspects of the analogy:
Firstly, if the stone was a random shape would it have less information in it than if it were intricately carved by a stonemason? Secondly, because the wet sand impression would be an approximation of the smooth sharp stone, has information been lost in the transference to the sand (comparing the information in the sand to that in the stone and not what you did (comparing the information in the stone to the info in the stone and the sand combined.))
Talkorigin states that one should be suspicious if anyone claims to measure meaning so Cubist's 2 examples must have the same amount of information because they have the same number of nucleotides. That wouldn't seem sensible to me if one were coding for a useful protein and the other was random. But from your viewpoint they are both random, right? With the former being a happy accident?
"Expelled" is a fictitious work of propaganda that is only believed by creationists. I wonder why "Pauline", who isn't a creationist, believes it.
I asked for evidence against evolution that is being censored. Not for an example of a chemist who does not understand biology.
"Pauline", you imbecile, that was not my quote.
Why are you asking me these questions? You creationists are the ones who claim to be able to measure "information" in such scenarios and are able to determine that it can only result from intelligence. So what "intelligience" caused the information, that you already admitted exists, to be contained in the shape of the rock?
So your answer to Cubist's question is that they both contain the same amount of "information", unless one of them contains more information than the other. Yeah, that answer makes a lot of sense. You creationists are such idiots.
@lutesuite
"I asked for evidence against evolution that is being censored. Not for an example of a chemist who does not understand biology."
I know the article I sent you was very long but if you had read down to the 4th white text box, then you would have seen a paragraph headed "The decline of academic freedom". That was the information you asked for.
It's rather strange that you are claiming that people are not persecuted for challenging evolution yet you have done nothing but persecute me, even when I am admitting ignorance and asking for your help to understand things. Do you teach at all in your role? Do you call your undergraduates "imbeciles" Do they learn better this way?
Here is a humble honest and clever man: http://www.jmtour.com/personal-topics/the-scientist-and-his-%E2%80%9Ctheory%E2%80%9D-and-the-christian-creationist-and-his-%E2%80%9Cscience%E2%80%9D/
I'm assuming that you would call him a creationist as his viewpoint is similar to mine. Can I ask if you DO understand macroevolution? Have you really got no doubts at all? No data that puzzles you? Do you also understand abiogenesis? Care to share?
You think I claim to be able to measure the information in genomes because you erroneously associate me with Creationists? How irrational. I've never claimed that. What I have done is ask if you know of a mutation that increases information and you told me about a rock and some wet sand. I didn't make the obvious comment as I do teach and I would never call a learner an imbecile.
So why don't we cut to the chase "Lutesuite"? You are clearly an intelligent man (all that testosterone kinda gives your gender away). You very confidently claim that "Expelled" is fictitious (even the parts where individuals were interviewed and were giving their perspective?) so you must be very knowledgeable to have come to that conclusion so confidently. I'm sure you wouldn't have dismissed it as Creationist nonsense without checking its accuracy.
So why don't you tell me the correct answer - which of Cubist's sequences contained the most information? And remember the rules: show your working (or should I say "show you're working"?) Or is it your view that there is no information in DNA?
@lutesuite: "So your answer to Cubist's question is that they both contain the same amount of "information", unless one of them contains more information than the other. Yeah, that answer makes a lot of sense. You creationists are such idiots."
I was DISCUSSING it with you, not giving my ANSWER to the question which is clearly and unequivocally this: "I haven't got a clue!"
Have you? xxxx
Well, gee, "Pauline", you've got me there. No, I don't know how to calculate a numerical value for the amount of information in a genetic sequence. I guess that means I can't make the claim that there is no mutation that can increase the amount of information in a genome.
Except, guess what, you moron: I'm not making that claim. You and your fellow IDiot Andy Wilberforce are. So if you don't know how to caculate the information in a genetic sequence, you can't really claim that it cannot be increased by a mutation. Can you? Well, I guess you can, because you just did. But you can't do it without revealing what a brainless fool you are.
Pauline,
James M. Tour (the fellow you linked to) admirably confesses his ignorance on some subjects, but it looks as if he hasn't gone far enough. In this he is, as you seem to say, rather like you. Neither of you has the knowledge required to decide between evolution and creation, but you both need to go that extra step and admit that someone else might. I do, for example. Yes, I understand macroevolution. Not completely -- nobody does -- but enough for our present purposes: I know that it happens, because I know that all species are descended from a common ancestor. The evidence is voluminous and conclusive. Would you like to know some of it?
John wrote: " I know that it happens, because I know that all species are descended from a common ancestor. The evidence is voluminous and conclusive. Would you like to know some of it?"
Yes John, please do share your best conclusive evidence.
Actually Pauline, it was me who wrote that. And actually, by Shannon's theory information was indeed transmitted from the rock to the sand. Where did you get that Shannon's would deny something this obvious?
The example for the rock was not written for you (I did not write that example, my explanations were more spectacular, but neither you or Andy want to acknowledge those explanations, lest you start misfiring more evidently than you already are). It was an example of non-biotic information-producing events (of which I also gave a spectacular one that Andy ignored by producing a red-herring). If you are interested read my example to you (biological increase in information by duplicated genes, but read it, don't assume it), and the abiotic one. In any event, I told you, there's an increase in information. Why should we ignore that the rock is still there in order to measure the information? Why should we take each apart? Just so that the creationist bullshit holds? Well, that hardly qualifies as scientific inquiry. If you truly wanted to learn, you would pay attention and question the creationist approach as much as you question the actual science. But I don't think you care. So far you have not tried to understand a single point. You just come with more and more creationist propaganda rather than listen.
So? More creationist propaganda, or at least a bit of trying to understand?
@lutesuite
"lutesuite: "Except, guess what, you moron: I'm not making that claim. You and your fellow IDiot Andy Wilberforce are."
cf: Pauline: "You think I claim to be able to measure the information in genomes because you erroneously associate me with Creationists? How irrational. I've never claimed that."
Are you having trouble keeping up?
Andy,
I'm going to back-pedal a little. Common descent happens at many levels, from pairs of closely related species to that last universal common ancestor, and the evidence is stronger for some parts of that big tree than for others. Since there was a whole lot of passing around of genes early on, the earliest bits of the story are less clear than they might be. Still, we have this: Theobald, D. L. 2010. A formal test of the theory of universal common ancestry. Nature 465:219-222.
However, anyone who doubts macroevolution as a whole must consider not just the first life but any relationships among species, however recent. I can't possibly summarize every little bit of evidence for everything. I can only present a sample. I'll give you a bit on whales and a bit on birds, the latter from my own research: Shedlock, A. M., M. C. Milinkovitch, and N. Okada. 2000. SINE evolution, missing data, and the origin of whales. Systematic Biology 49:808-817; Harshman, J., E. L. Braun, M. J. Braun, C. J. Huddleston, R. C. K. Bowie, J. L. Chojnowski, S. J. Hackett, K.-L. Han, R. T. Kimball, B. D. Marks, K. J. Miglia, W. S. Moore, S. Reddy, F. H. Sheldon, D. W. Steadman, S. J. Steppan, C. C. Witt, and T. Yuri. 2008. Phylogenomic evidence for multiple losses of flight in ratite birds. Proceedings of the National Academy of Sciences 105:13462-13467.
I hope they will stand in for the thousands of similar references, for countless parts and levels of the tree, that there is no room to provide. But read those first (they should both be easy to find on the web) and see what you think. You too, Pauline.
You should excuse Lutesuite's confusion because you're being confusing. Your request for a mutation that increases information makes no sense unless you suppose that information can be measured. (And in fact there are several attempted measures of information, e.g. Shannon information, but you don't accept them.) But whatever measure you want doesn't exist, and that makes your demand meaningless. Lutesuite, in his own warm way, is trying to explain that to you.
John, thanks for the links and especially for including the one about whales which I'm sure you know by now that I take a special interest in. I also appreciate that you're honest about there not being any conclusive evidence for universal common decent.
@negative entropy & the harsh man
"If you truly wanted to learn, you would pay attention and question the creationist approach as much as you question the actual science."
fyi I got the info about information & meaning:
Readers should be suspicious of any writing on the subject that:
•Claims to provide a measure for meaning;
from here: http://www.talkorigins.org/faqs/information/infotheory.html
:-)
@John Harshman:
"So? More creationist propaganda, or at least a bit of trying to understand?"
The latter please.
Gene duplication - that's 2 copies of the same information right? Until Natural Selection doesn't work on one copy, freeing it to mutate into something incredibly useful by chance. Someone sadly gave me Down's Syndrome as a great example of an increase in information. Can you send me something more uplifting?
@John Harshman
"Your request for a mutation that increases information makes no sense unless you suppose that information can be measured.
So who do you love more John? Me or your mother?
Now don't pretend that you don't love us exactly the same if you can't measure it.
Love you lots,
Pauline xxx
I also appreciate that you're honest about there not being any conclusive evidence for universal common decent.
I hope I didn't give that impression. There is conclusive evidence for universal common descent; it's just that there might have been multiple connected lineages exhanging genes at the start rather than a single lineage that branched -- a network rather than a tree. And these two hypotheses grade into each other: there seems to have been a network connecting a mostly treelike history in those early days. And it's become more treelike since then.
So, do you have any reaction to the publications?
But Pauline, I don't love you at all, and never will if you keep on as you are. You're sidestepping the question. I may not have a name for the unit of love, but I can certainly rank my feelings by strength. You, however, can't decide even such a relative ranking for DNA sequences. Or can you?
Can you send me something more uplifting?
Not until you tell me how I can recognize "more information" when I see it. According to Shannon information, duplicating a gene or a chromosome does increase information. So what measure do you have for which that isn't true? Trisomy 21 is also an increase in information in the genome. Who ever said that increased information had to make things better?
mutate into something incredibly useful by chance
That's exactly the sort of dismissive statement that makes people think you're a creationist, and an arrogant, dishonest one at that. Nobody says anything of the sort. The overwhelming majority of duplicated genes are lost. A few gain the rudiments of a new function, enough for selection to grab onto and hone into something useful. Does that sound like "by chance" to you? If so, you have no understanding of evolution. In fact you have a negative understanding, since you believe much that ain't so. You have to stop reading the creationist literature.
As for the quote from talk.origins, perhaps you should take it seriously.
John, my first impression is that it's not conclusive. The supposed strength of the argument is based on the assumption that SINEs do not have function, which is being questioned by many scientists. There are also inconsistencies among species regarding the presence or absence of a given SINE making it hard (impossible?) to determine their phylogenetic relationships. I saw some number on the unlikelihood of SINEs being present at the same loci in unrelated species, yet that is the case in e.g. deer and mice.
@lovely John
But I can. It seems obvious that there is more information in the human genome than a bacterial genome but how do I 'know' this? (and by the way is it true?)
I asked whether a purely random sequence would have less information in it than a sequence that coded for a real, useful protein. Common sense would suggest that the random sequence (or one with a repetitious pattern eg AGAGAGAGAG) has less information in it - wouldn't it? It feels more meaningful just like my love for my mother.
I do know that I'm using "information" here in its lay meaning and not the Shannon information definition - that's one source of my confusion probably.
Although trying to understand information theory has addled my brain somewhat - can you explain it simply to me?
And I ask again, do you think there is NO information in DNA?
On the topic of academic freedom:
In 2006, a professor of biochemistry and leading biochemistry textbook author at the University of Toronto, Laurence A. Moran, stated that a major public research university "should never have admitted" students who support ID, and should "just flunk the lot of them and make room for smart students."
Interesting.
I'm sorry, but your first impression is wrong. Nothing you say is right here. It isn't necessary that SINEs have no function in order for their pattern of insertion to be informative. Nobody that I know of thinks that SINEs in general have function, only that a few of them have acquired a function, just as any random mutation may. There are a very few cases of homoplasy in individual SINE insertions (and in some other retroelements too), but that doesn't change the picture, which is confirmed by a great many insertions as well as more conventional DNA sequence analyses. There is no mechanism for concerted homplastic insertions.
I'm afraid this is a standard creationist argument: if there is any homoplasy (what you call "inconsistency") at all, no matter how slight, phylogenetic analyses tell us nothing. You will have to do better than that.
@John Harshman
I said: "mutate into something incredibly useful by chance"
You commented: "That's exactly the sort of dismissive statement that makes people think you're a creationist, and an arrogant, dishonest one at that. Nobody says anything of the sort. The overwhelming majority of duplicated genes are lost. A few gain the rudiments of a new function, enough for selection to grab onto and hone into something useful. Does that sound like "by chance" to you? If so, you have no understanding of evolution"
So are you a closet Creationist? You are saying that mutations don't occur by chance in this paragraph aren't you?
Pauline,
Yes, there is more information (still using the Shannon definition here, for want of any better) in the human genome than in a bacterial genome, since the amount of information is closely related to the size of the genome, and the human genome is much larger. Then again, a typical fern genome by the same token would have much more information than that.
I'm afraid that "it feels that way to me" is not a very good gauge of relative information content, especially since different people have different feelings. The lay meaning of "information" is by no means clear, and it's hard to tell what you even think you mean by it. Science just can't work that way.
I can answer your question only if we agree on what "information" means. If you want my opinion, I don't think it's a very useful concept in talking about evolution, whatever the meaning. But what are you really trying to get at? Think about it before you reply.
Pauline,
That sort of dishonest playing with words doesn't present you as a seeker after truth, your supposed mission here, but as a seeker after points in some game of your own. No, I'm not saying that mutations don't occur by chance. I'm saying that natural selection doesn't occur by chance. Are you absolutely sure you have a degree in biology? This sort of thing is what leads to incredulity on the part of a reader.
John, some more sources for mistakes that I'm sure you are already aware of from the article "Perfect SINEs of evolutionary history?" that was published in Current Biology: " (a) An independent insertion at the same site in two different species is a convergence that introduces error into the phylogenetic analysis. (b) A precise deletion of an existing SINE is a reversal that also introduces error. (c) An ancestral polymorphism that spans successive speciations can be randomly fixed across species in a pattern that conflicts with their true relationships. (d) The loss of a primer-annealing site in a species by mutational decay prevents the PCR amplification of its targeted locus, thereby introducing missing data and ambiguity into the study. (e) The number of independent synapomorphies for a group can be over-estimated when different SINE insertions are derived from the same amplification event."
@John Harshman
I rather think you've got this backwards John. Point scoring is your game not mine.
You were the one who jumped down my throat and ridiculed me.
You said: "That's exactly the sort of dismissive statement that makes people think you're a creationist, and an arrogant, dishonest one at that. Nobody says anything of the sort. The overwhelming majority of duplicated genes are lost. A few gain the rudiments of a new function, enough for selection to grab onto and hone into something useful. Does that sound like "by chance" to you? If so, you have no understanding of evolution"
And to be fair I had only said "mutate into something incredibly useful by chance" so actually, it wasn't fair of YOU to accuse me of being dismissive, dishonest and arrogant for saying something basically true. Ironically you were being dismissive, arrogant and dishonest - I put it down to the fact that you are constantly second guessing what I am saying which is clouding your judgement - I don't think you are an imbecile.
Having respected your very sensible suggestion: "But what are you really trying to get at? Think about it before you reply." I would like to respond in the hope that you don't have another hissy fit.
The chance mutation bit is the bit I have the most difficulty with in macroevolution. Hence what I said above (see? that was honesty not deception.) I have no problem with Natural Selection acting once a beneficial mutation has occurred. I have no problem with genetic drift. I have no problem with loss of function through mutation. I just can't seem to believe that enough beneficial mutations would occur by chance and that each of them would have enough of a difference for Natural Selection to act on them, especially when looking at very complex systems (those that IDers call irreducibly complex). It seems that often we have to believe that some parts of a system evolved with no benefit until the final piece of the puzzle fitted in. The notion of increased information seems to help me verbalise why I can't believe it, but it may not be in the Shannon sense.
Dawkins' "climbing Mount Improbable" just doesn't do it for me. It's like saying OK I know that harmful mutations occur more frequently than beneficial ones, but if you just give it millions of years then enough beneficial ones will come along for Natural Selection to act on them (but many many more harmful ones will have destroyed you genome by then.)
So how do you believe the bit that I'm having trouble with?
Andy,
In the likely event that I get "bad cop" John instead of "good cop" John (who was quite helpful), can you help me? Do you have answers to the bits I find difficult?
I've only got out of date (30 years old) undergraduate level Genetics but I'm keen to learn!
You ask creationist IDIot Andy for help? But you;re not a creationist? Sure Pauline.
Well, since you're unable to read my examples and ways of getting a sense of the increase in information, I doubt that you care. You skimmed at most. You said that copies don;t increase Shannon's information when the opposite is true. I told you and you don't care. Typical. Creationist won't pay attention, and that's exactly what you do. You just give more and more creationist propaganda in exchange.
Bye "Pauline."
Yes, Andy, I know all that but the last one, and I'm not quite sure what that means. However, none of them do much to change the value of evidence from multiple SINEs, much less the independent evidence from ordinary sequence analyses. You are bringing up minor sources of uncertainty, not reasons to doubt the full analysis. Why do you confuse the two? I will speculate that you have a prior commitment to denying macroevolution. Is that it?
Pauline,
I'm really not trying to score points. I wasn't even ridiculing you. I'm trying to explain what your posting looks like to those who read it. You are not presenting the affect of an honest person looking for information. That impression may be false, but nobody here has any way of knowing except by reading what you post, and that's how you come across. You must understand that "mutate into something incredibly useful by chance" gives exactly the impression I'm talking about to any unbiased reader. No, what you said is not "basically true". That you think so is more evidence that you don't understand evolution. This isn't a hissy fit, just me pointing out what your words suggest. If you don't want me to get that impression, then you need to say something different.
Your difficulty in believing something is not an argument. Do you see that? You are also confusing macroevolution itself -- common descent of different species -- with its mechanism, the most important of which may be natural selection. We have much more evidence for the event than we have for its cause.
You clearly don't understand natural selection. I'm sorry that you think this is insulting, but it's just true. Harmful mutations are eliminated, usually without achieving an appreciable frequency, at the cost of a few deaths or loss of reproduction, while beneficial mutations are preserved and become fixed. Natural selection therefore works even if deleterious mutations greatly outnumber beneficial ones. And there are many ways in which mutation and selection can produce an irreducibly complex system, just not the way you mention. You really, really must stop relying solely on creationist sources. Did you even read Dawkins' book, or did you read about it on a creationist web site? I'm sorry again if you think that question is insulting, but it's a hypothesis suggested by what you say.
Maybe you should ask Robert Byers, too, "Pauline." He's actually stupider than you, if that can be believed, but he is at least more honest about his motivations and beliefs. And he's sure to give you an answer with which you can agree, even though it will certainly be incorrect, so that's the important thing, right?
Gosh, "Pauline", just when I didn't think you could become any more of a moron. What do you think was the "claim" to which I was referring in that quote? (Hint: It's not what you said it was, you buffoon.)
And is it really that hard for you to figure out how to use the "Reply" function here?
[part 1 of a 2-part reply]
sez pauline, who is not at all a Creationist, honest to god she's not, but who nonetheless just happens to present bunches of arguments straight out of the Creationist (Young-Earth in particular) playbook, and i am of course completely and unstintingly confident that her consistent use of (and credulity towards) Creationist arguments is just an innocent and extended coincidence:
Talkorigin states that one should be suspicious if anyone claims to measure meaning so Cubist's 2 examples must have the same amount of information because they have the same number of nucleotides.
This is the first time you've said anything about "meaning" in this thread, Pauline. "Information", yes, you've mentioned "information" a number of times. But "meaning"? Not so much. However, "meaning" and "information" are not the same thing, Pauline. Claude Shannon had a thing or two to say about the distinction between "meaning" and "information", to the point that he explicitly rejected any notion that the information theory he created, even could deal with "meaning".
You were making noise about "information", not "meaning", when you wrote "So not one example of a mutation that increases information ..?". You were making noise about "information", not "meaning", when you wrote "If feathers didn't evolve from scales then where did the DNA information to make feathers originate?" and "The term "evolutionary novelties" isn't very informative - practically, the DNA base pairs and information coded into them has to come from somewhere…". So if the topic you're really interested in is the question of how "meaning" gets into DNA… well… Let's just say that if your intent was to express your ideas clearly, your consistent-up-to-this-point use of the word "information", and equally consistent-up-to-this-point avoidance of the word "meaning", is highly counterproductive vis a vis achieving the goal of expressing yourself with clarity.
So.
While you haven't explicitly said so, Pauline, you nevertheless have raised a number of arguments which carry the unspoken presumption that random mutationscan't create information, which, in consequences, supports the hypothesis that you do, in fact, subscribe to that presumption. I mean, seriously, if you didn't think it wasn't possible for random mutations to create information, why the heck would you even bother to ask a question like "where did the DNA information to make feathers originate?", y' know?
Okay, there are alternative reasons why someone might ask such a question. Like for instance, someone who's kinda ignorant of biology might ask such a question. But you, Pauline, have made noise about your "Natural Science degree from Cambridge University, specialising in Genetics in the 3rd year", so either (a) you reject the notion that random mutations can be a valid source for the "information" in DNA, or (b) you're ignorant of biology (in which case, you lied about your degree).
[part 2 of a 2-part reply]
To repeat myself from a previous comment on this thread:
"Random mutations can't add information!" is very much a Creationist argument, so anybody who presents that argument as if it were evidence against evolution has no right to complain when other people treat them like they were a Creationist. That said, there is a simple way in which any person who makes the random-mutations-don't-create-information argument, can demonstrate that they aren't just yet another goddamn Creationist spewing yet another bogus Creationist non-argument: Measure the information content of arbitrary nucleotide sequences. Because if you can't measure the information content of arbitrary nucleotide sequences, on what grounds can you assert that 'information' cannot be created by 'random mutations'? If you can't measure the information content of arbitrary nucleotide sequences, how the heck can you tell whether or not Nucleotide Sequence X has more, or less, 'information' in it than does Nucleotide Sequence X-plus-a-mutation?
You say that there's more "information" in the DNA of humans than in the DNA of [insert other species here]? Fine. Don't just baldly assert that the DNA of humans has more "information" than the DNA of whichever other species, prove it—by measuring the "information" in the DNA of humans, and measuring the "information" in the DNA of that other species, and comparing those two pieces of data. But I see that you've already acknowledged that you have no friggin' idea how to measure the information of arbitrary nucleotides: "…my ANSWER to the question [is] unequivocally this: 'I haven't got a clue!'" Well, props to you for admitting you're clueless. Can we take it as read that you will no longer raise arguments which include the unspoken presumption that random mutations can't create information, nor ask questions which are built on that unconfirmed presumption… or at least, you won't do so until after you've educated yourself to the point where you can answer a simple question re: which of two arbitrary nucleotide sequences has mire "information" in it?
That wouldn't seem sensible to me if one were coding for a useful protein and the other was random. But from your viewpoint they are both random, right? With the former being a happy accident?
"Accident" implies unlikelihood. Now, the last time I checked, the Earth is home to something like 10^30 bacteria. Given that bacterial genomes tend to consist of no more than 10^6 base pairs of nucleotides, with the occasional statistical outliers ranging as high as maybe 10^11 base pairs, it seems likely that there exist real-world instances of every physically possible mutation that can affect bacterial DNA. So if all mutations actually do occur, exactly how big of an "accident" is it that some particular mutation, that has some particular consequence, might occur?
Yes. And math departments flunk students who think the square root of 9 is 1000. Blatant discrimination!
@lutesuite
Actually yes. The reply link isn't working for me, it returns me to the top of the home page...
I just clicked on the "Reply" under your message, and here I am. Some computers do seem to have trouble with the Blogspot formatting, though.
@lutesuite
"Yes. And math departments flunk students who think the square root of 9 is 1000. Blatant discrimination!
Well that's actually on the syllabus. Your faith or worldview should not be relevant if it doesn't change the way you do science. The large number of famous Christians who were outstanding scientists is evidence that believing in God doesn't mean you can't do great science. Some were even creationists.
You have just conflated belief in God with creationism. Why? Larry didn't propose flunking Christians, just IDiots. There's a big difference, which creationists seem not to understand, and that's another bit of evidence that you are a creationist.
Well that's actually on the syllabus.
Last I heard, evolution was on the syllabus too. Your point?
The large number of famous Christians who were outstanding scientists is evidence that believing in God doesn't mean you can't do great science. Some were even creationists.
Nobody, not even Larry, has claimed that Christians can't be scientists. But I would be interested to know which great scientists were creationists. Could you name some of them? You would have to include only those scientists who had compared evolution vs. creation as scientific hypotheses, though. No counting Newton, who lived long before evolution became an issue. Louis Agassiz is the only one who comes to my mind. But who else do have?
John you claimed to have conclusive evidence that all species are descended from a common ancestor. It took me about 30 minutes to google sufficient material to establish reasonable doubt to the best evidence that you had to offer. I did not come back saying that I had disproven your point and I do not claim to know the reach of evolution, yet you say my mind is made up because of prior commitment...Sure, I'm a creationist, but creation could have happened so many different ways. I very much doubt that Pakicetus and Basilosaurus share a common ancestor because it would violate the mathematical laws of probabilities to get the mutations needed for the morphological change and specialization fixed in the time available. If I would be confronted by conclusive evidence that it happened then I would have to conclude that biological life has built in teleology, an idea that I don't favor, but I'm prepared to go where the evidence points.
"Last I heard, evolution was on the syllabus too. Your point?"
My point is that IDers can study the theory of evolution (as they should) and pass exams on it without believing it actually happened. Unless they wanted a career limiting choice of being a conscientious objector.
John: "Your difficulty in believing something is not an argument."
I get it (at last) you are using this blog to argue. Well I'll be darned I wanted to learn something through discussion.
http://creation.com/creation-scientists
" You would have to include only those scientists who had..."
and who says you get to make all the rules?
Now how about answering my question which you dodged: do you think that there is no information in DNA?
P.S. You would have to answer in whichever way you felt like at the time.
If they can study it without believing it, in the face of all the evidence they will encounter, there's something wrong. Except in very rare cases, of which I know exactly two, creationists have grossly misunderstood evolution. As you do, for example.
You get nothing, I'm afraid. You show no sign of being interested in learning. You say you want to learn, but I and others have tried to teach you quite a bit without any apparent success. You in fact tend to ignore substantive points. I ask you to search your own motivations and ask yourself if you're being completely honest with yourself here.
Now, an argument isn't a bad thing, and it certainly isn't mere trading of insults; it's a reasoned series of propositions to advance a claim. Science is all about argument. You need to pay attention to the arguments if you want to learn anything.
I don't get to make the rules, but you don't either. Go ahead and mention your creationist scientists, and I will explain to you why they're invalid as support for your claim. Why mention creationists at all, by the way, unless you're trying to defend creationism?
To answer your question (and I will point out that you almost never answer mine): yes, there is information in DNA, or at least we can think of it in that way. Each nucleotide is two bits of Shannon information. But I do not think that word means what you think it means.
@cubist:
I said:
"It seems obvious that there is more information in the human genome than a bacterial genome but how do I 'know' this? (and by the way is it true?)"
To which you curiously retorted:
"Don't just baldly assert that the DNA of humans has more "information" than the DNA of whichever other species, prove it"
To assert = "to state a fact or belief confidently and forcefully"
Didn't you spot my question in the brackets? I was asking if it were true. (I'm also not bald by the way.) Why do you accuse me of asserting it? (I apologise if English isn't your mother tongue.)
So I understand how frustrating it must be for IDers (even the bald ones) to assert that information cannot increase by random mutation if they can't measure it, but you can't prove they're wrong if you can't measure it either. But I do get the point that it isn't you doing the asserting.
So my question to you is: Do you think that there is information in DNA? Can you measure it? Is the concept even helpful (John thinks not I seem to remember.)
@John
"(and I will point out that you almost never answer mine)"
Sorry, tell me which questions you've asked and I'll answer them. I thought most of your questions were rhetorical like "don't you know how stupid you are?"
The answer to that one is yes by the way. The more I learn the more I realise I am ignorant.
"hanks Pedro - finally some useful information! I have educated myself as you suggested. That's really interesting that scientists now believe that feathers didn't evolve from scales - that claim had always made me very suspicious and now it makes much more sense. I noticed that the evidence for the very first feathers was the most lacking: "little information is available on the ontogenetic development of early feathers." Do you know of any research that covers this stage (maybe not yet as these references were all very recent)? If feathers didn't evolve from scales then where did the DNA information to make feathers originate? Does anyone have any hypotheses?"
So no evidence I am here to learn John.
Are you going to get back to me about intermediate neck lengths of giraffe ancestors? Or do you think that the neck could possibly have lengthened over time very quickly leaving no fossil evidence? (For the benefit of clarity this is a question not an argument.)
Pauline,
I think you need to go a bit further in your realization of ignorance. But it's certainly a worthy goal. It's hard to find just what question you haven't answered, as your responses are not attached to the posts they're responding to. You need to fix your browser. But I will try.
Here are some of them:
You have just conflated belief in God with creationism. Why?
Louis Agassiz is the only one who comes to my mind. But who else do you have?
Did you even read Dawkins' book, or did you read about it on a creationist web site?
I would be interested in the estimates you have of the probability of life evolving; show your work, please.
You seem to be getting all your information from creationist sources. Why?
So, do you have any idea how new species might arrive? If not evolution, what's your alternative?
In addition to your other problems, you don't realize that "differ by at least 150 million nucleotides" doesn't mean 150 million mutations. That figure (and where did you find it?)
No, evolutionary theory doesn't predict phyletic gradualism. Why would you think so?
Yes, I understand macroevolution. Not completely -- nobody does -- but enough for our present purposes: I know that it happens, because I know that all species are descended from a common ancestor. The evidence is voluminous and conclusive. Would you like to know some of it?
According to Shannon information, duplicating a gene or a chromosome does increase information. So what measure do you have for which that isn't true? Trisomy 21 is also an increase in information in the genome. Who ever said that increased information had to make things better?
The overwhelming majority of duplicated genes are lost. A few gain the rudiments of a new function, enough for selection to grab onto and hone into something useful. Does that sound like "by chance" to you?
Finally, this isn't a question, but it's a point you have consistently ignored every time I've brought it up: As I've said before, the major evidence for macroevolution lies in comparisons of DNA sequences, largely the fact that they agree on phylogeny.
You have just conflated belief in God with creationism. Why? Because I was making the point that faith shouldn't reduce scientific ability so creationism and belief in God both share supernatural belief so it wasn't important to make that distinction at that point.
Louis Agassiz is the only one who comes to my mind. But who else do you have? I sent you a link to this which you seem to have overlooked.
Did you even read Dawkins' book, or did you read about it on a creationist web site? I have read all of Dawkins books starting with The Selfish Gene which I read at University. The man is one of the reasons I find evolution hard to believe in and why I came looking for real scientists to give me real answers. I didn't find what I was expecting.
I would be interested in the estimates you have of the probability of life evolving; show your work, please. I could cut and paste an answer from a Creationist publication but I thought you'd rather I didn't.
You seem to be getting all your information from creationist sources. Why? I'm not. I'm reading both sides. I gave you a quote from Talkorigins - is that an undercover Creationist site? But there's no point me asking you questions about evidence FOR evolution because we would agree on that. I repeat I'm here to learn and Pedro taught me something. I also learned that this debate is way too full of emotion than it should be if it were an objective scientific forum.
So, do you have any idea how new species might arrive? If not evolution, what's your alternative? I don't have one and neither do you. Just because there isn't a better theory YET doesn't mean evolutionists should lie about evidence against evolution. If the theory's all that then it would stand up afterall.
In addition to your other problems, you don't realize that "differ by at least 150 million nucleotides" doesn't mean 150 million mutations. That figure (and where did you find it?) I gave you the reference already. You don't care.
No, evolutionary theory doesn't predict phyletic gradualism. Why would you think so? Because initially evolutionists thought so (before PE) because mutations were thought to be random events which, followed by natural selection would predict gradual change. I know thinking has progressed, but this is why Darwinian evolutionary theory predicted PG just like I said it did. PE was data driven not theory driven.
Yes, I understand macroevolution. Not completely -- nobody does -- but enough for our present purposes: I know that it happens, because I know that all species are descended from a common ancestor. The evidence is voluminous and conclusive. Would you like to know some of it? Yes please - didn't realise this was a genuine offer given your tone. I have already read about sequence preservation and also that different evolutionary trees are derived by studying different genes. I'd like to know more. Like evolution's answer to how the LUA came about, and abiogenesis. Also I'd be interested in just one reference that has given you personally the most doubt in evolution and why you think it is ultimately wrong.
According to Shannon information, duplicating a gene or a chromosome does increase information. That's why I don't think Shannon information is my problem. I want to know how DNA changes account for a new limb / novel structure by chance. 2 genes coding for the same thing doesn't mean an increase in that sort of information. So what measure do you have for which that isn't true? Trisomy 21 is also an increase in information in the genome. Who ever said that increased information had to make things better? That is a rhetorical question not a real one.
The overwhelming majority of duplicated genes are lost. A few gain the rudiments of a new function, enough for selection to grab onto and hone into something useful. Does that sound like "by chance" to you? The chance bit comes in with the change in sequence to form a new functioning gene (you do agree that this bit would be by chance mutation don't you?) then the new function has some sort of selection advantage or is fixed in the population by genetic drift (another bit of randomness) So yes "by chance" is a good term here.
Finally, this isn't a question, but it's a point you have consistently ignored every time I've brought it up: As I've said before, the major evidence for macroevolution lies in comparisons of DNA sequences, largely the fact that they agree on phylogeny. This is also used as an argument for a common designer. And isn't it true that some events have been assumed to have happened twice (at very low probability) in very different species?
Now how about sending me the intermediate neck length giraffe data? It's for my daughter's school.
I'm clicking here: Subscribe to: Post Comments (Atom) to read your comments. Clicking on the orange arrow next to your name sends me to the original page where I cannot post because it's overflowing.
How is the fact that noncoding genomic elements between separate lineages conform to phylogenetic patterns predicted by evolutionary theory evidence for a "common designer"? Any brain dead moron can parrot creationist talking points. Actually understanding them is another matter.
@lutesuite
Noncoding genomic elements between separate lineages conforming to phylogenetic patterns is the strongest evidence I've come across for evolution - for me personally. There's still some interesting disagreement between well-respected molecular biologists about the details and I'm less convinced about some convergent evolution reasons to explain some similarities that are unexpected. You may know of more convincing evidence which I'd be glad to hear of.
I do worry about the Evolutionary worldview restricting curiosity (especially in schools, hence my request for a giraffe of intermediate neck length to reassure me that the UK government haven't made a huge mistake in using giraffes to teach evolution to primary school kids.)
I also worry about stuff like this:
"Although the proposed phyletic branching patterns for ratites do not correspond perfectly to the order of separation of land masses during the breakup of Gondwana, the convenient serendipity of continental drift as a mechanistic explanation for ratite distribution proved irresistible and it stands today as a textbook example of vicariance biogeography"
So the data doesn't fit the proposed mechanism well, but I want it to fit so badly and I don't have a better mechanism so it becomes a "textbook example". I guess that evolutionists do this because creationists attack them if they are truthful that there is some doubt, but this is a positive feedback loop with each side getting more and more arrogant and vicious towards the other. I admire the truth in the above quote and wish it were more widespread.
@lutesuite
How is the fact that noncoding genomic elements between separate lineages conform to phylogenetic patterns predicted by evolutionary theory evidence for a "common designer"?
Because the functions of the non-coding sections are designed to be similar for similar lifeforms?
Pauline,
When quoting, you should try to set off the quotes somehow or your post becomes hard to read. Italics would work. So would quotation marks. Thanks for answering some of those questions, however poorly. It's a start.
But now I'm at a loss how to respond. This thread has become terminally unwieldy. I'll just pick the last bits.
This is also used as an argument for a common designer. And isn't it true that some events have been assumed to have happened twice (at very low probability) in very different species?
Yes, phylogenetic trees have been used as an argument for a common designer, but a little thought should convince you that it's a bad argument. Why should separate creation result in a nested hierarchy? Of course, there are well-known mechanisms by which trees from different genes may not match, but they match to the predicted degree; again, this doesn't fit any kind of separate creation.
Now how about sending me the intermediate neck length giraffe data?
I know nothing about fossil giraffids. You may be confusing me with someone else. I will however point out that if okapis were unknown to science, you would probably consider them to be intermediate neck length giraffes.
I want to know how DNA changes account for a new limb / novel structure by chance.
They don't. Selection clearly plays a large role in the evolution of new structures. And most "new" structures are just modifications of existing ones. "New" limbs, for example, are modified fins.
[Regarding evidence for macroevolution] Yes please - didn't realise this was a genuine offer given your tone. I have already read about sequence preservation and also that different evolutionary trees are derived by studying different genes. I'd like to know more. Like evolution's answer to how the LUA came about, and abiogenesis.
If by "LUA" you mean "LUCA", then that as well as abiogenesis is a different subject from macroevolution, one I don't have much expertise in. Some questions in macroevolution are easy to answer and some are more difficult. On easy questions, different genes usually give the same answer. On difficult questions, you have to work hard on analysis. But the conflict has been seriously overstated by creationists. You really shouldn't pay so much attention to them. Here are a couple of fine references I gave to Andy a while ago, ones you should easily find on the web. Are they convincing?
Harshman, J., E. L. Braun, M. J. Braun, C. J. Huddleston, R. C. K. Bowie, J. L. Chojnowski, S. J. Hackett, K.-L. Han, R. T. Kimball, B. D. Marks, K. J. Miglia, W. S. Moore, S. Reddy, F. H. Sheldon, D. W. Steadman, S. J. Steppan, C. C. Witt, and T. Yuri. 2008. Phylogenomic evidence for multiple losses of flight in ratite birds. Proceedings of the National Academy of Sciences 105:13462-13467.
Shedlock, A. M., M. C. Milinkovitch, and N. Okada. 2000. SINE evolution, missing data, and the origin of whales. Systematic Biology 49:808-817.
That is indeed a common creationist idea. But have you ever really thought about it? Probably not, since you offer it up as an explanation. Remember, first, that most of those non-coding sections are junk; they have no function. Even within functional bits many of the changes don't matter; silent changes in protein-coding genes, for example. Besides, the most anatomically similar species are sometimes not the most genetically similar. Whales don't have fish genes; they have cow genes. Now why would that be?
Pauline,
Where did you get that quote? I would actually agree with you that using ratites as an example of vicariance is a bad idea, but it sounds as if the person being quoted is saying that too. There was indeed a big movement in favor of vicariance a few years ago, and it went way overboard. But you really shouldn't accuse scientists of lying to keep creationists off their backs unless you have evidence of such a thing. Which you don't.
The alternative explanation, by the way, is dispersal and local extinction, for which there is some fossil evidence.
Hee hee. You'll never guess where it comes from, John:
http://www.pnas.org/content/105/36/13462.full
Oh. I swear I don't remember writing that bit. Bet it was one of Ed's, and of course it's in the introduction, which is just setting up the big surprise. I would prefer "Nevertheless, no proposed phylogeny, ours included, can be explained entirely by the order of separation of Gondwanan fragments.
Multiple losses of flight, with the implication of greater dispersal capability for ancestral paleognaths, make a strictly vicariant model less compelling. The existence of volant paleognaths in the Paleogene of Europe and North America also suggests that dispersal must be considered (45, 57). Dispersal of ratites is further suggested by phylogenies in which the extinct moas of New Zealand are not sister to the extant kiwis (2, 10, 11), as would be predicted by strict vicariance. Thus, fossil data confirm that simple vicariant models can be rejected." and "Finally, our phylogeny removes the need to postulate vicariance by continental drift to explain ratite distribution. Although that theory seemed to represent a consilience between evolutionary biology and geology, it was never completely consistent either with any published phylogeny or the existence of paleognath fossils in the Northern hemisphere (45, 57). Perhaps the impact of our phylogeny should be viewed as yet another example of the phenomenon that Huxley called 'the great tragedy of science—the slaying of a beautiful theory by an ugly fact.' ”
Pauline should pay special attention to that last sentence.
I should probably admit that the last sentence isn't mine either. It's either Mike's or Ed's. And Huxley's, partly.
Let's not overlook "Pauline's" not-so-subtle insinuation, of course, John: That your own research refutes evolution and you're just trying to cover this up by making excuses and engaging in unwarranted speculation, so that you won't be "Expelled" by the Darwinian orthodoxy.
But she says she's the one who's being insulted here...
Andy,
read again: those are minor sources of noise. John said:
However, none of them do much to change the value of evidence from multiple SINEs
Try and understand that before going to the next sentence ... Got it yet? No? OK let's wait a bit more ... Got it now? Shit Andy! OK, maybe this other part will clarify:
You are bringing up minor sources of uncertainty, not reasons to doubt the full analysis.
Got it? Do you know what the word "minor" means don't you? You don't!
So, now that you've got it maybe you'll understand why I face palmed when you wrote this:
It took me about 30 minutes to google sufficient material to establish reasonable doubt to the best evidence that you had to offer.
No Andy, minor sources of uncertainty are not reasonable doubt.
I would suggest that you read the article instead of the abstract, but that would be too much to ask if you didn't catch that those were minor points even after John said it so succinctly.
@John Harshman
lutesuite has just given you a good example of a scientist lying. (I'm assuming he is a scientist...)
He said I was insinuating that:
"your own research refutes evolution and you're just trying to cover this up by making excuses
Naughty little tinker!
How can this: "I admire the truth in the above quote and wish it were more widespread" possibly be termed "insulting"? I was clearly talking about confirmation bias. Scientists see what they want to see based on their own worldviews.
You yourself have said to me: "But you really shouldn't accuse scientists of lying to keep creationists off their backs unless you have evidence of such a thing. Which you don't."
In fact I have accused scientists AND creationists of lying but your own confirmation bias has only heard me accusing scientists.
And I do have proof. Piltdown man.
But more currently Mary Schweitzer backtracking about her discovery of red blood cells in T-Rex bones as soon as the Creationists got on her case.
And your paper "Phylogenomic evidence for multiple losses of flight in ratite birds" was really good. Very informative. (If you're listening lutesuite I read his paper - to learn - got that?)
Andy,
You have admitted your prior commitment. Now all you have to do is admit that this commitment gives you a strong bias against accepting the evidence. You like the occasional bit you can interpret as arguing against whale evolution (though in fact those bits generally do not) and ignore the weight of the evidence.
I would like to see your work on the improbability of common ancestry for Pakicetus and Basilosaurus, but I suspect you just made that up. Am I right?
But let's face it: you have been confronted with conclusive evidence; you just continue to grasp at all the straws you can find. I could cite the DNA sequence evidence, but you'd just quote a paragraph about the potential pitfalls of sequence analysis. But isn't it a wonder that all the errors point in the same direction?
And I do have proof. Piltdown man.
Proof of what? That scientists routinely lie?
By the way, who exposed that particular fraud? Scientists or creationists? And who committed it in the first place? The main suspect is Dawson -- an amateur archaeologist, not an evolutionary biologist.
But more currently Mary Schweitzer backtracking about her discovery of red blood cells in T-Rex bones as soon as the Creationists got on her case.
What exactly did she backtrack about? Last time I checked, she still believed they were genuine red blood cells. She never claimed that their preservation meant that the T. rex fossil should be dated as recent (if that's what you're trying to insinuate). Its age is beyond dispute for reasons that have nothing to do with evolution.
Pauline,
I don't understand why, in order to complain about you accusing scientists of lying, I must also complain about you accusing creationists of lying. I don't really care if you accuse creationists of lying (though it's a hard thing to prove). But I do care if you accuse scientist. There is the occasional hoax, true. But you're going for something quite different: wholesale lying for a particular reason, to respond to creationists. I don't see the lying, and I don't see the response. All in your head.
If my paper was very good, did it convince you of the reality of macroevolution? If not, why not?
John, it seems to me that you have a commitment to reductionism even though mind and cosmos speak against it. I'm willing consider all evidence even those pointing beyond materialism, I don't see how that would be a handicap.
Andy, I have no idea what I have said here that implies a commitment to reductionism. If there's evidence pointing beyond materialism, I'm willing to consider it. But I don't see how that applies in any way to the evidence for common descent. I'm not even (at least in this thread) arguing against guided evolution. I'm merely arguing for descent with modification, however the modification is achieved. You appear to be arguing for separate creation, and that goes way beyond any question of materialism or whatever is its alternative.
Let's recap: you have claimed to know that common ancestry of whales is improbable, but ignore calls to show your work or even to explain your reasoning. You have claimed that my evidence is questionable, but have mentioned only one paper whose point was that SINEs are not absolutely perfect characters. I can see only the abstract, but I bet the take-home message of even that paper wasn't that SINEs are poor guides to phylogeny, only that they aren't magic. And I bet Miyamoto also made the point that finding multiple SINEs would greatly decrease uncertainty. I suspect, in fact, that you were quote-mining that paper. Am I wrong?
All you're saying here is "I know you are, but what am I?", but I have reasons, well explained, for my conclusions about you. What do you have about me that suggests I'm not looking at the data objectively?
Richard Buggs calculated that we know, for sure, that only 84.38% of the human genome (as a whole) aligns to the chimp genome. He thinks 95% can turn out to be true, but he does not think it will. Assuming 85%, we have a difference of 15%. That is about 10 times 1.4%. Thus, by your calculations we would have the fixation of 1210 mutations per generations.
Did I miss something?
(Of course I am assuming Buggs is right)
http://richardbuggs.com/2018/07/14/how-similar-are-human-and-chimpanzee-genomes/
Buggs (and others) are looking at large deletions/insertions in the two genomes. If the human genome has a 5000 bp duplication that's not present in the chimp genome then they calculate this as 5000 differences. That's not an accurate measure of the similarity and it's certainly not a number that's relevant in calculating mutation rate. That's because the duplication is a single mutation event and not 5000 separate mutations as you and Buggs imply. This is why we only look at stretches that can be aligned and why we emphasize single base pair mutations.
".. as you and Buggs imply"
Who am I to imply anithing? LOL
Thank you, Larry. Really appreciate your comments. :)
(I finally found your answer. What was wrong? I just had to load more comments. LOL)
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