Charles Jackson: Expert on ERVs

What do you know about the "Birthyday paradox," and how or if it is an issue in this ERV discussion.

Get back to me on that...

I *heart* U abbie! When you tear apart one of these idiots it gives me a warm fuzzy inside :-)

Edit by ERV to remove less-than sign in heart symbol, thus deinvisibleize comment, lol!

Thank you! I had no idea the ubiquitous "heart" emoticon would cause such a problem. Note to self: escape all html entities, even when speaking. That way I don't forget!

William: okay, the suspense is killing me and i won't wait until erv answers you: what is the connection?

The "birthday paradox" is 1) not a paradox at all, and 2) really not relevant here.

Also, at it's most basic, the birthday paradox doesn't work, because birth rates tend to fluctuate during the year. The initial assumptions of the basic calculation are 1) Nobody was born on Feb 29, and 2) Equal distribution of birthdays. The first can safely be assumed, and doesn't change the calculation very much. The second, however, greatly changes the matter. There is a spike in mid-summer, and another in December/January. See http://www.nytimes.com/1990/10/02/science/seasons-sway-human-birth-rate… for a discussion of this.

Of course, none of this matters to Limp Willy. His Limpness simply *hates* the idea of anything that proves evolution. He has an ideological bias that blinds him to any and all evidence that would conflict with his preconceived notions.

Besides, "The magic sky-fairy done it" is just simpler than actually thinking.

If you have 23 balls and 365 tubes in a bundle and you drop the balls randomly, you have a 50% chance one tube contains 2 balls. This way you avoid the "birthday part" and all its peculiarities.
And it is a paradox, just like Olber's paradox: a simple question with a complete unexpected answer.
William, enlighten me, is it relevant in this discussion?

Did he really insert the Comic Sans on his own?

Sili-- 100% original.

Comic sans, words mashed together, misspellings, hot pink-- I can take a screen-shot for unbelievers.

Hot pink is hot.

But wait! What about the birthday paradox? What does the birthday paradox have to do with ERVs and Charles Jackson? I'm dying to know!

Brian: correct me if i am wrong. Are you trying to ridicule me?

Are we allowed to call people Fucktards here at ERV? If so, I'd like to state for the record that Charles Jackson is a Fucktard.

If not, I apologize, and would instead like to state for the record that Charles Jackson is a Cum Stain.

Well, that was a pretty well done take down. Just two remarks: First, I think you are unfair to him for saying "sex cell" instead of "germ line." If one is speaking to someone who doesn't know much they will likely get the meaning of "sex cell" but would need explanation of "germ line." Also, if you are going to nitpick about germ line aren't there a few cells other than sperm and eggs that are germ line cells like gametocytes?

Also, I've never fully understood why so many people dislike Comic Sans. But I'm self-aware enough to know never to use it. Apparently Jackson is not.

Also, William, I'd also like to hear how the birthday problem has anything to do with this. I'm a number theorist not a probability theorist but I'm pretty sure the answer is "not related at all."

Wow. This is why the pursuit of science is so important for christians, athiests, and any other beleif system alike. New findings on ERV should conclusively show that many creationists need to revise their beliefs, at the very least.

See, now *this* is why I love this place! From Eddie Janssen: "just like Olber's paradox". I learned something new. I was not familiar with Olber's paradox. I had to look that one up... fascinating.

Anyway, those aren't really "paradoxes" in the classic sense, which is what I was using. "All Cretans are liars" said the Cretan, is a paradox. I suppose those are mathematical paradoxes (paradoxi?) but not being a math geek...

Anyway, my (and Eddie's) point still stands. It is irrelevant to this discussion, and typical Limp Willy trying to toss a complete red herring into the discussion.

Man, I get long-winded sometimes. Shorter: Eddie is right, I learned something new, and Limp Willy is an idiot.

Jeez, ***I'M*** not an expert in ERVs by a long shot, but I have picked up more listening to you, Abbie, than this guy.

So far, all the creationist responses to the ERV evidence that I have seen amounts to nothing more than hand waving. Most of them don't even seem to grasp the subtleties of the evidence. It is something that takes some deep thinking to grasp, and we all know how good creationists are at deep thinking (NOT).

And once again Wallaids tries to intimidate people with a cryptic though still obviously ill-informed objection to evolution. This guy is starting to look like a one trick pony.

Also, since no one seems to have guessed what Wallace is trying to say, I'd say that he's trying to draw an analogy between the likelihood that others in a room have the same birthday with two different species having the same retrovirus in their genome. If that is even close to his claim, he's comparing the sample space of days of the year to the sample space of retroviruses and possible insertion sites. Comparing apples to trucks, in other words.

He sure has a wacky way for using comic sans. It's like he had to think of a new way for showing emphasis. He's got like 100 different methods for showing emphasis. Anyway, you can easily see why he's creationist. Lot's of confusion going on up thar in the ol' cuckoo's nest.

ooohh, I think I get the birthday "paradox" problem. I think he means that ERV insertion events can be like birthdays, and that two species can have the same ERV insertions without implying common ancestry, just out of sheer chance. I guess he also implies that since ERV insertions are nonrandom that helps his argument.
I contemplated calculating the "common birthday" probabilities considering orthologous genome positions, number of insertions etc, but I don't think the homology is valid: the birthday problem refers to the probability of two persons in a group having the same b-day. What is the "group" where we are considering ERV insertions here?

Now, now... let's be fair. WW didn't say birthday paradox, he said birthyday paradox. I have no idea what a birthyday is, but maybe it's relevant.... or not.

Mobius, I don't think the basic idea is that hard to grasp at all. And ERV at one point (was it with in the debate with Jackson? I don't remember) introduced the analogy with the chewed Lego. That analogy makes it so concrete that the basic problem should be clear to pretty much anyone.

Well, Abby, if you've ever wondered why Creationists insist they know so much about these things, look no further:
http://gagne.homedns.org/~tgagne/contrib/unskilled.html

It appears to be a general human trait: when we don't know stuff about one subject or other, we tend to be vastly overconfident about how good we are at it. I do hope that people like you and I, people who have learned what it's like to gain expertise in one area (for me: cosmology) have learned about these sorts of pitfalls and are more able to be a bit wary of trusting ourselves for areas we know we are not experts in. Creationists, well, most of them have never learned to be experts in anything.

The Birthday paradox is just a name. The idea can be applie to randome events.

I guess he also implies that since ERV insertions are nonrandom that helps his argument.

Make up your mind. They are either random or they're not.

WW spouting nonsense :

The Birthday paradox is just a name. The idea can be applie to randome events.

No it can't.
Go to work next Monday,ask 23 people what their birthday is,and there is a 50:50 chance you will find 2 people with the same one.
How this would,in any way.shape or form,be related to ERV insertions,is beyond anyone with more than 2 operational brain cells.

William!
From Wikipedia:
The birthday problem can be generalized as follows:

1.given n random integers
2.drawn from a discrete uniform distribution (all values of a finite set of possible values are equally probable)
3.with range [1,d],

what is the probability p(n;d) that at least two numbers are the same?

Which numbers should we use to answer your original question in your first comment? (assuming 1,2 and 3 are met)

William,

I do see the point you are trying to make: the solution to the "birthday paradox" explains why seemingly surprising events (50% of all randomly chosen groups of 23 people have at least one pair of individuals with the same birthday) is actually what would be expected based on the laws of probability and chance. It's an interesting topic because whoever solved the "paradox" actually did the numbers to *prove* that what is observed is contrary to what our intuition might expect.

Thus, your alluding to the birthday paradox is a claim that the distribution of ERVs in humans and chimps is yet another example of such a phenomenon. Specifically, ERV distribution MIGHT seem to be (on a common sense or intuitive basis) inexplicable unless humans and chimps have a common ancestor, but in fact CAN BE adequately explained as a highly probably event between any two unrelated species when one models the problem mathematically.

One distinction between a "denialist" and a true "skeptic" is that the former will be satisfied with any hypothesis that can be constructed that confirms their preconceived notions, regardless of how strongly it is supported. Whereas the honest skeptic will go the next step and do the hard work to rigorously test the hypothesis to prove the point. (An example of the former: a climate denialist merely tossing out "variations in solor output" and then walking away from any discussion of global warming).

The irony of your contribution on this topic is that, so far, you are illustrating the general phenomenon that Abby is criticising in her post: you seem to be claiming expertise in this area and have hinted that your expert analysis of the ERV issue negates the conclusions that the biologists are making from the data.

AFAIK, you might have a good argument on the topic, but only if you show us the numbers (just like those that support the solution to the "birthday paradox"). Unfortunately, I rather suspect you don't have the goods. I really think you have satisfied yourself that the biologists are wrong merely because you can think of a hypothesis that *COULD* prove them wrong *IF* that hypothesis were to be rigorously tested and shown to be correct.

In otherwords, you're denialist, not a skeptic, and you are not really interested in an intellectually honest consideration of the issue.

Wait, I thought WW was opposed to the idea that events could occur through random chance.

Wallace, define 'random'.

If an ERV is placed in the genome at a position impossible to predict, but only a limited number of positions have a good probability of fixing in a population, is the existence of that ERV in a subsequent species random or not?

Is there such a thing as pseudo-random?

That was a very interesting 'debate'. The lego analogy was nice, although I think you could have tied it in with the nested hierarchy as evidence against a common designer.

Jackson appears to be an incredibly sneaky and dishonest creationist, but it's fascinating to see how shaky this creationist edifice is becoming; the more evidence piles up, the more absurd and self-contradictory their rationalisations are becoming. Just think about how bizarre their position has become - their defence of a literal interpretation of Genesis now seems to hinge on the esoteric specifics of retroviral biology. This may satisfy the professional creationists but I don't have the feeling that the creationist in the street will be impressed by such arguments.

For the first time ever, I had a distinct sense that this creationist bullshit is going to come tumbling down one day. Maybe not in our lifetimes, but it seems too absurd to sustain itself indefinitely in the mainstream of public life.

If an ERV is placed in the genome at a position impossible to predict

Not able to predict and random are not necessarily the same thing. ERV insertion may be stochastic with bias (e.g., akin to a weighted die), but you can still do probability analysis even in the real world scenario described by LanceR in #5. That is, if you know P(Jan. 1), P(Jan. 2), through P(Dec. 31), you can calculate the probability of two people in a randomly selected group having the same birthday, even if P(M)!=P(N). Or you can simply model it as random process as Eddie Janssen describes in #6. And you don't need to stick to a population of 23 with 365 pigeonholes, either.

Is there such a thing as pseudo-random?

Yes, there is such a thing. But I don't think anybody on Abbie's side is asserting that ERV insertions are pseudo-random, as pseudo-random implies intelligent algorithms.

In the real world, humans have 50-60 almost complete HERVKs, and chimpanzees have ~20 of the same family. Of the chimpanzees 20, most of them are orthologous with humans, and a few inserted after the human/chimpanzee split, making them chimpanzee specific, leaving me to estimate on stage that we shared ~14.

So Abbie, to make such a claim, surly the number of viable pigeonholes has been determined, or at least estimated. Likewise, the number of successful ERV insertion events is known. What are these numbers for chimpanzees?

Admit you dont know, investigate the answer later, and get back to them. Really get back to them-- dont just say you will.

I guess there will be a post on this later, describing the mathematical analysis, and not just arm waving, that shows it really is improbable that chimps and humans are not related based on ERV evidence alone. (The Birthday paradox shows that arm waving doesn't fly. E.g., an English professor puzzled that over half of her classes of 25 students each have at least two students in the same class that share a birthday isn't really that surprising to a math professor).

Clearly, Abbie, you believe that the probability of humans and chimps sharing the HERVKs they share through chance is so infinitesimally small that they must be related.

I'll wait for you to investigate the answer to this question, and describe your analysis.

Eddie Janssen@11:

Brian: correct me if i am wrong. Are you trying to ridicule me?

Holy cow, not at all. That was a sincere question! I honestly couldn't see what WW was getting at. But now that it's been explained by several posters -- and confirmed by WW himself in #31 -- I now understand. The argument goes -- correct me if I'm wrong:

1. Birthday Paradox is initially surprising.
2. Ergo, math is hard.
3. Ergo, I don't believe you got the math right up there.

Can you believe I failed to grasp that chain of reasoning from WW's initial post? Gee whiz.

My mistake, I got a bit sensitive as your post seemed to repeat my post (post nr. 4). In the Netherlands that often indicates that the first one is being mocked. Sorry

Ok I'll bite: assuming random insertions, 3e9 base pairs in a haploid human genome. The probability of a particular random insertion would be 1/3e9. If we assume the chimp genome to be roughly the same size, give or take the duplications, we have the same probability. So, for a random insertion to occur in both genomes in orthologous spots: 1/3e9 x 1/3e9 = 1/9e18. for this to happen 14 times ~ 1/2e262. I think that's very close to 0, so even if you throw in the additive probabilities of the ones that do not coincide, it still leans overwhelmingly towards common ancestry.

"I don't think anybody on Abbie's side is asserting that ERV insertions are pseudo-random, as pseudo-random implies intelligent algorithms"
I think that's bullshit but I'll bite too. What I think you mean by pseudo-random is that insertions occur not at random but with some preference for particular regions, like, say, heterochromatin or gene promoters. These are usually determined by the chromatin context, ie the integrase interacting with heterochromatin protein 1 or having a interaction domain to direct it to particular histone modifications. That does not imply "intelligent algorithms", only selection, as usual. Probably selection against trashing the host genome. Even so, it is only a preference and not a preference for particular positions in the genome, only regions.
Lets propose a hypothetical ERV with a preference for the 2-300 bp upstream of protein coding genes, for instance. In the human/chimp genome there is a low-ball estimate of 20000 genes, that's 20000 x 200 = 2e6 available positions. 1/2e6 for a particular position, 1/4e12 for the same insertion in both species, ~1/4e172 for 14 of them. Which is, again, pretty close to 0.
BUT this argument is not the birthday problem. The birthday problem would be : "given a set of species with orthologous genomes and 1 or more random ERV insertion, what is the probablity that two or more of them will have the same insertion and how does it depend on the size of the set". I don't think the birthday problem is the one you want to apply here, and I don't think talking about probabilities helps your argument. By the way, what is your argument? So far you've only cryptically alluded to a mathematical problem and asked Abbie to report back.

Eddie: In this case I suspect it really indicates that I hadn't read your post thoroughly....

(I like your re-visualization of the Birthday paradox, btw. I'll have to remember that the next time I find myself explaining it.)

Come on, William, don't hold back. Show us your calculations that have utterly convinced you that ERVs really are analogous to the "birthday paradox" issue.

Mikka has taken a stab at it, and here is mine:

Given 60 complete ERVs in Humans and 20 in Chimps, and assuming that there are X number of "spots" in the genome where ERVs can possibly insert, what is the expected number of homologous spots that have an ERV in both human and chimp?

For any X, the probability of any spot having an ERV in human is 60/X, and 20/X in the chimp. The product of these two is the probablility that any given homologous spot has an ERV in both species. Multiply that by the number of spots to get the average expected total number. (It reduces to 60 x 20 / X)

Further, how many spots would there have to be to give an average of 14 common ERV in homologous locations? Here's what I get when I assume different values of X:

If X = 20,000, expected average number = 0.06
If X = 3,000, expected average number = 0.4
If X = 1,000, expected average number = 1.2
If X = 300, expected average number = 4.0
If X = 100, expected average number = 12.0
If X = 85, expected average number = 14.1

BTW, these numbers would have a SD that's approximately the square root of the value, so 8 is the target number if you are looking to get within 2 SD of 14. And that would be at an X value of 150. Which roughly equates to an average of only 6.5 "spots" per chromosome.

So, there are two sets of calculations for you. If you don't like some of the assumptions made, tell us what *YOU* did. You swagger around here as if you have already done the math and know the answer, so put your version on the table. Either put up or STF up.

I eagerly await William's calculations. A nice back of the envelope calculation like those above would be an excellent first step.

Let's forget the fact that it is vanishingly improbable to share 14 insertion sites (like Divalent said, if you think I'm wrong, I'd love to see some math). If "ancient" ERVs are just different insertion events and have nothing to do with common ancestry, why is it that, over and over and over again, the nucleotide substitutions in the proviral sequences lead to phylogenetic trees that match up with the trees that we have for the primate lineage? And both the 5' and 3' LTRs do this, even though the substitution sites are completely different between the two.

(I'm tempted to say that, if you don't understand why agreement between the two LTRs is important, you should really try doing some reading before telling scientists they're wrong. But I'm feeling generous, so... At the time of insertion, due to how retroviruses reverse transcribe RNA, the LTRs are identical. It's possible, but extremely unlikely, that the ERV phylogenetic tree exactly matches the primate tree simply because it has evolved host specificity. However, if you have 5'LTR matching substitutions in chimps/humans that you don't have in bonobos and the same matching pattern for the 3'LTR but completely *different* substitution sites, then the insertion event predates the bonobo/human/chimp split. Period. Because that 5' LTR was identical to the 3'LTR when the virus inserted. And for *different* substitution sites between the 5'/3'LTRs to just somehow manage to recapitulate the host phylogenetic tree over and over and over and over again is next to impossible. This is beautiful evidence for common ancestry that just makes you completely wrong, William).

Brian, Abbie says that we don't need to match it up with any other data. It speaks for itself. (Something about a pillow case full of something or other.) So I won't go off on that tangent right now, though it could be interesting in the context of confirmation bias.

Per her post, still waiting for her to get back to me on that math stuff, and the underlying assumptions.

I'd love to see some of you argue with a peer reviewer. (~"No, I say it's random, improbable, etc. You prove me wrong or STFU. Besides, you use funky fonts. And you quote papers much better than I paraphrase them." Waves arms wildly.)

"Brian, Abbie says that we don't need to match it up with any other data."

Compare it to what data? You want some regression model where ERV presence in the genome is compared against every possible thing in the universe until we've eliminated them all as possible cofactors? In other words, prove a negative? If you think there is some mechanism, some hidden variables, etc., then it is your job to produce data verifying it/them/whatever.

"Per her post, still waiting for her to get back to me on that math stuff, and the underlying assumptions."

Last time I checked, it was you who brought up the birthday paradox and asserted (via your usual cryptic circumlocution) that it had something to do with retroviral insertions into the genome. Therefore it's up to you to do the math. And handwaving by glibly asserting that the same principles apply to all random processes won't work. The relatively banal probability calculations behind the birthday paradox apply specifically to a uniform distribution of birthdays (AFAIK).

The birthday paradox doesn't seem all that relevent to me.

This is mostly because the ERV evidence for common descent isn't just the locations of the insertions; it's the content as well. Given that there are many possible ERV DNA sequences, getting *similar sequences* in the same place in two different species really points quite hard to a single insertion event.

Describing this in terms of the original birthday paradox goes something like this: Suppose you had a class of 30, and 2 of the children shared a birthday. Then you did a DNA test and the results indicated that the two birthday-sharing kids had the same parents. Two explanations spring to mind:

Explanation 1: Twins.
Explanation 2: "Coincidence! Birthday paradox!! How do you know birthdays are random?"

I like the first one better.

"I'd love to see some of you argue with a peer reviewer"

Peer reviewers don't throw around cryptic, misleading, and almost entirely irrelevant statements in order to obfuscate the issue at hand. Peer reviewers don't pose as intellectuals and make pompous remarks to bolster their shallow, deluded egos. Peer reviewers don't demand answers to questions and ignore the answers they are given and instead keep demanding that answers are given. Peer reviewers tend to have relevant expertise in the area in question instead of being anonymous internet schmucks with a metaphysical axe to grind.

To summarize about 1/2 of the comments here:

WW: Abbie you must show me your math I think you're wrong cause goddidit
Others: WW, here's some numbers, now show us yours that say science is wrong and goddidit
WW: I was talking to Abbie so nany nany boo boo

Yes, there is such a thing. But I don't think anybody on Abbie's side is asserting that ERV insertions are pseudo-random, as pseudo-random implies intelligent algorithms.

This rubs me the wrong way on all counts.

First of all pseudo random is in CS defined as a sequence of numbers appearing random but aren't - often being generated with some sort of seed number and pseudo number generators will produce the exact same sequence of numbers with the same seed.

Pseudo random isn't random with constraints to the domain. That is still completely random.

Second intelligent algorithms???

Wazzat!!!?

Some kind of algorithms that learns, makes art and politics?

An algorithm is an automata. Some input producing some output nothing more nothing less. It's not intelligent in any sense of the word.

Processes in nature can work according to a set form og events producing some form of output from some form of input and can mimick the behaviour of an algorithm og algorithms can be constructed to mimick natural processes, but that has nothing to do with how the processes in nature occured or that algorithms we use for instance in CS or math to solve problems are designed by us assuming some kind of intelligence.

The only way we can prove algorithms is intelligently made is because we can prove authorship.

Don't forget the nested heirarchy.

Wee willy is implying the ERV common insertions might be random coincidence of the same insertion in humans and chimps - some 14 (or 96, or thousands) times, with the same site and sequence.

That alone is stunningly improbable, as shown by the back-of-envelop calculations above.

But then, Gorillas and Humans, and also Gorillas and Chimpanzees, share some 11 of those. So wee willy has to also show how having the identical location and insertion happen 11 times in Gorillas, in additin to the 14 identical insertin sin humans and chimpanzees, is a not-improbable random event.

And then so on through the Orang, Gibbbon, old world monkeys, new world monkeys.

And then he has to further show that it is a not-improbable random event that the pattern of nested heirarchy in the ERV insertions sites and sequences matches that derived from genomic DNA sequence, protein similarities, morphological similarities, physiological similarities, and so on.

But then, wee willy isn't interested in showing any of this. He is only interested in uttering cryptic implications that don't actually mean anything, but that he hopes might sound meaningfully challenging to the evidence for common descent to someone who doesnt know enough yet to know better.

The denialist tactic is stunningly similar across disciplines. Hell, it might even imply some degree of common descent. Divalent at 27 nailed it.

Take a close look at Wallace's arguments. He isn't claiming improbability, he's claiming impossibility. His point is that having 2 ERVs in different species is not impossible so Abbie's argument that ERVs are sufficient in themselves to evidence common descent is wrong.

His purpose is to create doubt about Abbie, not to argue against evolution. It's nothing more than a petty creationist tactic.

Re: 39

What? Where did Abbie say that it was simply the insertion site that was important? Also, what?! We're ignoring corroborating data now and dismissing it as tangential? I know that's how good scientists do their work.

Also, fuck you. If the 5'/3' LTRs did not match up in terms of substitutions, that would be evidence against evolution. Except that they do. So you know where you can put your confirmation bias.

It's not that I don't believe you, Erv.

It's just I was stunned by this remarkable display of truth in adverticing - or lack of selfawareness.

way to make abbies point ww. fail to understand the math, make an obvious but notionally obscure reference to a simple result in probability -- which in fact proves the other partys points -- and claim victory. all while illustrating your basic ignorance and proving the legitimacy and point of the original article.

win! win!

even if you just wanna pretend to be a scientist, you still need to do actual work now and then to make sure you understand the underlying issues. otherwise, youre merely putting your ignorance up for all too public ridicule. doing this in response to an article raising exactly this point is an own goal of perfection. calling you an idiot would be redundant -- and an understatement.

/es

Maybe people share birthdays not because of magic sky-fairy design, but because people prefer to fuck on certain days.

You know what sexual intercourse is, right WW? Or do you believe that the stork delivers babies, too?

Correct me if I'm wrong about this, but I seem to recall that we share 98% of our DNA with chimps, and 15% of our genome is retroviral in origin. So that means that in addition to 14 of our 55 complete ERVs, we also share most (at least 13/15= 87%) of our ERV fragments with chimps. I suspect the amount of shared retroviral material is closer to the 98% of the rest of the genome that is shared, however.

The creationist is likely to (intentionally or not) confuse complete ERVs with ERV fragments. Perhaps it is best to mention stats for both, since both would seem to support evolution.

...Miranda?

Are you comparing the creationists with the Alliance? The Alliance is far less cartoonish than this bunch. And they have technically competent people.

Nice take down as always.

I been watching creationism since the mid-1980s and the degree which they are simply willing to make up stuff never ceases to amaze.

And I don't see how even non-random ERV insertions would help them very much as ERVs are just the start of the "plagiarized errors" problem which they have. I can't even imagine trying to count how many ways the gene for making vitamin C could have gotten taken out (insertion of something in the middle, deletion, duplication of part of the sequence, reversal of part of the sequence, point mutation(s) makes enough of a change to disable it, etc. And yet we and the chimps had the exact same thing happen? Multiple this by thousands of other examples.

Has any creationist really seriously addressed this? The usual response by them seem to be try to change the subject. One might as well as a young-earth "geologist" how Horseshoe Bend formed.

"CREATION TRUTH FOUNDATION"

I was not aware that the erstwhile Herr Doktor Professor Jackson C.O.D., A.A.A.(knight aspirant of the royal society of science Hobos {Nation of Sealand}), was part of that nest of YEC goofs out of Noble, Oklahoma and Arkansas.

Can I get confirmation on this.

I thought he was just your run of the mill IDer and not part of that group that runs the over sized garden shed with plastic fossil replicas and a Tower of Babel made out of matchsticks or whatever.

Did his "Points of Origin" internet ministry die off?

Last I heard he was operating out of a P.O. box in Kentucky and guest scribbling for "answersingenesis.com" and the IRC.

What happened?

Ideological dispute?

Money fight?

Sex scandal?

Has he been deemed the successor to Warlord G. Thomas Sharp and his Eureka Springs land gravate (Ignoramopolis)?

Inquiring minds......

@William Wallace:

Not able to predict and random are not necessarily the same thing.

I would argue they are. First, let me break the problem of probabilities into a few parts. First, consider macro phenomena that are modeled through probability, e.g. rolling dice or drawing cards.

When you roll a die, it's trajectory is uniquely determined by its angular and linear momentum, extension, mass density function, etc. There is nothing random about the outcome, except that it is exceedingly difficult for human beings to track or predict the moment-to-moment trajectory of the die. In principle, there is almost certainly an algorithm one could run on the output of a high-speed camera to determine the outcome of the toss of a die deterministically. In practice, we have to treat it as random.

Similarly, when a deck of cards is shuffled, the order of the cards is definite and the value of the top card is not a random variable -- it is a static value. However, the constraints of human sensory apparatus make it impossible (or very difficult) to keep track of this order. Thus, while the order of the cards is determined, it can be usefully modeled as random.

So in both these cases, the assumption of randomness is absolutely the result of an inability to predict, contra your assertion.

How about the expressions of phenotypes? Limb-length, eye or hair color, etc: properties of organisms that seem randomly distributed (usually approximately normally distributed) at a macro scale? Any half-way decent probability class should inform you that the approximately normal distributions are probably the result of the fact that such features are the product of hundreds or thousands of tiny little mechanisms operating deterministically and non-randomly, but independently. That is to say, any such phenotypic expressions are results of cells dividing until they receive a signal to stop, or of cells producing a certain protein in a particular concentration. All deterministic -- non-random -- at a micro scale. However, it is impossible to trace the millions, billions, trillions of interactions that ultimately determine these properties at a macro level, and so once again, we speak of probabilities -- merely because of the limits to our powers of prediction.

Finally, just a quick note on phenomena that seem random a priori, or in principle: quantum mechanical phenomena. These seem to finally separate the notions of unpredictability from randomness -- but do they? Not really. For one thing, perhaps we simply don't understand the nature of causality at this scale; that quantum interactions are in principle predictable, but we lack any models with the power to do so. Again, we have a situation where randomness is simply a matter of inability to predict, again, contra your assertion. But I don't agree with this. I find the uncertainty principle compelling; that it is, in principle, impossible to simultaneously predict the position and momentum of any body. Thus, the randomness once again comes directly from our inability to predict, or at least shows no obvious means by which the two concepts could be differentiated.

I argue that randomness is exactly an inability to predict, contrary to your assertion, and I have made a case for it. I look forward to your response.

I have to admit, one of my favorite things on the internet is watching the spine crushing body slams this community throws on limp Willy every time he shows up. Keep it up.

Not able to predict and random are not necessarily the same thing.

...

I argue that randomness is exactly an inability to predict, contrary to your assertion, and I have made a case for it. I look forward to your response.

You can argue all you want, but all you'll get is what you already got: in some cases it is, in other cases it's not. Hence the keyword necessarily.

An assumption is not what is, btw. Neither is a model. I've gone over this before on other threads. I have illustrated cases, such as so-called quantization noise, where we are able to predict a value, and yet that value is usefully modeled as a stochastic process. But the useful stochastic model doesn't take away from the fact that we already know we are dealing with a deterministic process. Quantization error = value before quantization - value after quantization.

But I'm glad you impressed Ty.

Any word on Abbie's calculations yet?

Didn't you know? She's waiting for Charles Jackson to present his calculations. After all, he was the one who actually made math claims.

Of course, you could act as his proxy, Limp Willy. Oh wait, we've already acted as ERV's proxies. In that case:

TITS or GTFO

Two little things, Limp Willy:

1. Burden of proof. You made the extraordinary claim. Back it up.

2. TITS or GTFO!

When last the topic of ERV's came up here, WW claimed to be working on a computer model to show that a nested hierarchy pattern could arise just by chance, without common descent. How'd that work out, Willie?

How'd that work out...?

Aside from your utter inability to comprehend and paraphrase what it was I was working on, it worked out better than initially expected. But, like the birthday paradox, it is not that surprising upon reflection. Indeed, the model does show that a nested hierarchy can be found that supports common descent, but that other hierarchies can also be found if sought. It even shows that if you start out with a well mapped out genome, and look for patterns there in less well mapped genomes, you will find the nested hierarchy that confirms what you are looking for. Strange, huh? But, upon further analysis, rather unsurprising.

The project was put on hold for the summer but I do plan to refine the models that generated the data. Of course, I am willing to admit, unlike many of you, that the premises often determine the outcome in science and modeling.

But, an interesting question question is, if nested hierarchies that go against common descent were found in the lab, would they be published? Who could possibly publish them before they were expelled, before the author and peer reviewers are outed as closet anit-Darwinians, or worse (at science blogs), politically conservative Christians?

Something to think about.

Who needs math when you have a good story? is the motto of the macro evolutionists.

Care you, you know, show us the results? What did you use to do the modelling? Is their source code available? Otherwise it is hard to take this seriously.

So, you have results, but need to refine it, what needs to be refined at this time? What have you implemented so far?

I have also been wondering about this whole expelled thing lately. If peer-reviwers are not willing to let papers that disagree get published, where are all the rejected papers? I'd be very interested in seeing those, along with the comments made by the reviwers.

Who needs math when you have a good story? is the motto of the macro evolutionists.

Bwahaha. I saw a bit of math in this thread, Wally; none of it was from you.

On the other hand, I saw some funny stories in this thread, and all of them were from you (I have a magic com-pu-tar program that disproves evolution! here's my imaginary fantasy of how scientists would react to my magic program!).

Who needs an irony meter when Wally's around? is our motto here.

Limp Willy:

1. You got nuttin, and you know it.

2. TITS or GTFO!

@William Wallace:

You can argue all you want, but all you'll get is what you already got: in some cases it is, in other cases it's not. Hence the keyword necessarily.

Typical creationist response to an interesting question: "I already KNOW the answer!"

An assumption is not what is, btw. Neither is a model. I've gone over this before on other threads. I have illustrated cases, such as so-called quantization noise, where we are able to predict a value, and yet that value is usefully modeled as a stochastic process. But the useful stochastic model doesn't take away from the fact that we already know we are dealing with a deterministic process. Quantization error = value before quantization - value after quantization.

My thesis, again, is this: a random phenomenon is exactly the same thing as an unpredictable phenomenon. Above, you simply repeat one of my arguments: that the assumption that a phenomenon is "random" is used when it is impractical to use a deterministic model to predict the precise outcomes. Usually, restating one of your opponent's arguments is not an effective counterargument.

Maybe you should define "random." I am tempted, but I suspect that if I try I will be accused of begging the question. I will consider any evasion or attempt to dismiss the definition of "random" as irrelevant or mere semantics as you conceding the point, because there is no reason not to define terms here. Defining "predictable" would also be helpful.

After defining random, you still have to provide one example of either:
A) a phenomenon that is random but not unpredictable, or
B) a phenomenon that is unpredictable but not random.

So good luck with that.

Okay, there's some argument about randomness here, and I think I need to inject a comment.

To qualify as random does not require outcomes to be equally likely.

If I roll two six sided dice and sum them (like I was playing Monopoly say), the total is random but not equally likely (7 is much more probable than 2 or 12).

Retroviruses insert randomly (in the sense that different sites have some chance of being the site that gets an insertion) as opposed to individual sites being specifically targeted.

This could be tested in the lab - you can infect a bunch of cells with identical genomes with the same retrovirus and see the retroviruses insert in different places each time.

However, each site is not necessarily equally likely to be an attemtped insertion site, and not every attempted insertion has an identical probability of being "successful", both for various reasons.

So the random insertions are not (nor should we expect them to be) perfectly uniformly distributed over the genome. But if you do the experiment a hundred times, you'll see a different insertion point each time.

Random.

Using being not-equally-likely as an argument for nonrandomness is, frankly, dumb.

Using being not-equally-likely as an argument for nonrandomness is, frankly, dumb.

...and therefore exactly what we've come to expect from Limp Willy.

BTW, Still waiting for the math, Limp Willy.

Using random as a synonym for ignorance is almost as dumb as LanceR's blockquote usage. Most of you don't know how to solve the Maxwell-Faraday equation, but that doesn't mean inductors are random noise generators. And it didn't make the relationship between EMF and magnetic flux a stochastic process even before James Maxwell discovered the relationship. It was never a stochastic process, whether or not humans understood the underlying relationship.

Using being not-equally-likely as an argument for nonrandomness is, frankly, dumb

I agree. See #5 above, where LanceR did exactly that, while missing the point altogether. How dumb can one be, LanceR?

And efrique, where can you point to any statement I made that not being equally likely means something is not a stochastic process? You can't, hence, one can only conclude that you're being deceitful.

Using being not-equally-likely as an argument for nonrandomness is, frankly, dumb

I agree. See #5 above, where LanceR did exactly that, while missing the point altogether. How dumb can one be, LanceR?

So, Wally can't do math or read. Is there anything you are good at, Limpy?

Besides providing us with cheap entertainment, of course.

So, Limp Willy, can you do anything other than insult a broken blockquote tag? We're still waiting for your Amazing Magic Math(tm).

Math, or GTFO!

@William Wallace:

Using random as a synonym for ignorance is almost as dumb as LanceR's blockquote usage. Most of you don't know how to solve the Maxwell-Faraday equation, but that doesn't mean inductors are random noise generators. And it didn't make the relationship between EMF and magnetic flux a stochastic process even before James Maxwell discovered the relationship. It was never a stochastic process, whether or not humans understood the underlying relationship.

If this is a response to me, you're beating up a straw man. Let me try to clarify what it is I'm saying. Consider the following propositions:

A: Phenomenon P is random.

B: Phenomenon P is unpredictable.

I'm saying A iff B. You have the privilege of defining randomness and predictability. Once you do this, you can disprove my argument quite easily by either showing that there exists a P such that A and not B or B and not A.

Now, you rightly say that the assumption of randomness does not make phenomenon random. That is to say, we could have a P such that not A, and yet still get useful results by assuming A. That's not at issue. We still have P such that not A. If, for that P, we had that B is true, my argument fails. But I don't see how that would be possible given any reasonable definitions of randomness and unpredictability. I certainly can't think up any counterexamples, but I'm willing to believe that this is simply a lack of imagination on my part.

All in all, I think the distinction between unpredictability and randomness is a distinction without a difference. Parsimonious, don't you think? The only thing necessary to knock it on its ass (also, the only thing sufficient to knock it on its ass) is a counterexample.

So now that I have made it utterly clear how you can win this argument and given you the distinct advantage of defining the terms being used in the argument, are you ready to stop wanking and actually make a case?

This is the "Birthyday" theorem as proposed by Scrabcake

People like to have sex in winter because it's cold outside in the northern hemisphere. Staying inside is boring but you can get warmer by snuggling...
People like to have sex in winter because it's crazy hot outside in the populated areas of the southern hemisphere. Staying inside gets boring, and a person has to entertain themselves, especially if the only AC is installed in the bedroom.
People like to have sex in the fall because they get more work holidays that don't involve visiting relatives in the fall. I mean, Columbus day == perfect time for romantic getaway.

Therefore, in first-world western countries, there are more babies concentrated in the summer and early fall months.

This is something that is seemingly random, oh, like ERV integrations and evolution. However, it is guided by logical guidelines and rules that shift the probability of an event happening in favour of summer months to the determent of winter months. Therefore, the probability of two people with the same birthday in one room is not like the probability of getting two ones when you roll 3 dice, or like the probability of a tornado going through a junkyard and assembling a buick or whatever. It's more like the probability of assembling a buick with a whirlwind when there are only two pieces of the buick and they're magnetized.

"Most of you don't know how to solve the Maxwell-Faraday equation, but that doesn't mean inductors are random noise generators."

As others have noted, you need to define "random". One definition that is especially appropriate in this case is an output that can't be effectively compressed by a deterministic program on a Turing machine (i.e., the outcomes of successive rolling of die). You'd be familiar with this if you actually sat down and read about Kolmogorov complexity. How's that going, by the way?

The second part of the above was the "Randome Principle of Randomeness."

But wee willy has Secret Math (tm).

Secret Math (tm) is the best and most powerful kind - conclusions asserted by means of Secret Math (tm) are indisputable, can never be disproved, and therefore are true and correct by simple assertion, always.

You just have to have Faith (also tm).

I think I understand what William is thinking here. He is treating the individual infections as having no identity other than being an ERV in a specific location. In such a case you calculate in a similar situation to the birthday problem, treating potential infection sites as days of the year and individual infections as birthdays of individuals. You are calculating the odds that an infection in a different species occured in the same site. But even in this case the calculations are for 14 pairs of matched birthdays, not just two. And unless I am wrong the individual ERV infections are all unique as well as occurring at unique sites. Thus we return to calculating the odds of each individual ERV infecting the same spot in different infections, to the at least 14th power.

In short, epic fail.

He is treating the individual infections as having no identity other than being an ERV in a specific location. In such a case you calculate in a similar situation to the birthday problem, treating potential infection sites as days of the year and individual infections as birthdays of individuals.

Absolutely correct, MaxDWolf. When the reality is more akin to a teacher who discovers that 7* kids in her class share a birthday, February 2nd. In her second period class, she finds another 7 who have a birthday on February 2nd. Third period, fourth period, same story. This obviously can't be "random things appearing to be non-random". She begins to think "Maybe some of these kids are related". She then finds out that those kids are all from families who belong to the local pagan group, and Beltaine was celebrated on May 2nd the year they were all born. 9 months later, a miniature baby boom boosted the population.

So a seeming "birthday paradox" turns out to be anything but.

Of course, Limp Willy will come in to lie about his position, and probably insult my blockquoting again in order to avoid any substantive discussion of the issue.

*a number I pulled from a deep, dark place where I keep all such numbers... don't ask <grin>

I still think the funniest thing we got from Willy was that earlier thread, where he attempted to argue that ERVs inserted in specific locations by citing a paper which showed that they insert at thousands of different locations. Phantom math is also pretty funny but direct autopodifusilation is the best.

Just to make sure I understand what's going on with reverse transcription:

ssRNA is used as a template to create dsDNA. Its called reverse transcription.

So the viral capsid gets into the cell and releases ssRNA into the cellular matrix. And then that ssRNA molecule blunders around until it finds a DNA molecule into which it can insert itself. Having no will or volition, it doesn't make circles like a dog looking for a comfy place to lie down -- it just floats around until the conditions are right for the transcription reaction to take place, which could hypothetically happen just about anywhere on any of the chromosomes.

When this happens to a cell that is not a germ line cell, the new DNA will not be passed down to future generations, and so it is not a proper ERV. If it does happen to a germ line cell, then there are a few possibilities: the transcription could take place at a point in a chromosome that ruins some totally important gene and makes the germ line cell unviable. Otherwise, it might find a place in the genome where it can insert itself without ruining anything important, in which case it will get passed on to the offspring and become a proper ERV.

This explains both the assumption of randomness and the fact there are areas in the genome where one is more or less likely to find ERVs. We can't predict where in the genome the ssRNA is going to try to transcribe itself -- it's a function of Brownian motion and therefore pretty much unpredictable. BUT there's a lot of places on the genome where you can't put some viral DNA and expect to get viable offspring still -- so we can predict that the ERV won't end up in those places. We can't predict exactly where the ssRNA is going to get transcribed, but we can figure out where it's unlikely -- and therefore where it is likely.

Is this the idea?

LanceR:

Actually, it's more like you have a grad school teacher in a class of 25 where the same two same students have the same birthday and the same wedding anniversary. Now that two students have a birthday in common or an anniversary in common is not that unusual, but the same two students having both in common? It's likely that something's going on, e.g. twins having a double wedding, or two people who originally got interested in each other because of the birthday coincidence and got married, but both kept their original surnames (to make connection not too obvious).

Personal trivia: My paternal grandparents had the same birthday. They got a daughter as a birthday present one year.

@InquisitiveRaven:

That's an good analogy, too! Even better than mine. But you didn't blockquote anything! What will Limp Willy have to criticize?

While I agree that the birthday paradox doesn't properly apply in this case, there is a modification that is analogous. Given 'x' sets of girls with unique birthdays (ie, each set of girls has one or more girls with the same birthday) and 'y' sets of boys with unique birthdays [and a year of 'd' days], what is the probability that there will be at least one day that boys and girls will be celebrating their birthdays? For ERVs, 'x' and 'y' are the number of sites that a particular ERV family have inserted and 'd' is the number of possible sites. The formula (assuming no bias in insertion probability) if 'x' is less than 'y' (swap 'x' and 'y' if 'x' is larger) should be:

p = 1 - (((d-x)!) / ((d-(x+y))!)) / (d^y)

Back in the previous thread (Lentiviruses: Zaboomafoo Part Two, in April), cprs made a big hullaballoo about possibly orthologous PtERV sequences. At the time, I actually did start thinking about the issue in terms of the birthday paradox, but the thread died before I could fully develop my thoughts on it. Limp Willy's resurection of this concept prompted me to review my notes and finish developing my thoughts.

To recap the issue cprs brought up: a study looked for PtERV-1 in various apes. It discovered that humans and orangs did not have these ERVs, but gorillas, chimps, and other primates did. It then took ~160kb chunks that contained PtERV-1 insertions from the gorilla, chimp, macaque, and baboon genome and aligned them against the human genome to find unique insertions. Almost all insertions were unique to a particular species, but there were 12 pairs that were shared. This does not mean that these were orthologous, as the size of PtERV-1 averages to about 5% of the size of the genomic chunk and may merely represent an "overlap". The distibution of potential sites does not create a nested hierarchy that matches the accepted phylogeny - for any given pair of species, there are between 0-3 potential orthologous pairings [0,1,1,2,3] that contradict the accepted phylogeny if they are not overlaps.

So the question is, how likely is such an overlap to occur by chance?

Each species has about 75 PtERV-1 insertions. So we'll set 'x' and 'y' to 75. What do we set 'd' to? Well, the primate genome size is ~3Gb, and the chunks are ~160kb, so that gives us about 18,750 chunks that could harbor an insertion. Setting that as our 'd', we get p = 36% - which means that it is not all that surprising to find overlaps in chunks that large. Include insertion bias and other factors, and the results are basically what you expect. In fact, on the ones we could check, they were simply overlaps.

Now back to Wee Willy Wanker. In the case of more or less complete ERVs that are orthologues, we have confirmed these are not simply overlaps. The chunks aren't ~160kb wide, they're approximately the size of the ERV itself. That means the 'd' term increases by a factor of 20, and to make things even worse for Billy-Bob, the 'x' and 'y' terms are significantly smaller. My calculator crapped out trying to make that calculation - the number is very, very small.

"William Wallace's" argument/style seems very similar to Warren Bergerson's claim to have disproved evolution using actuarial math. He made this claim for more than 3 years on ARN and elsewhere and despite hundreds of requests that he show the work, he never would, merely claimed that he know it was correct.
It finally came out that he had NEVER DONE THE MATH, but he just 'knew' what the reulsts wouild be and so didn't have to.
Creationists supported him. But an actual semi-intelligent moderator on ARN banned him for lying. For three years.

Ala...

So, as usual, cowardheart displays his credentials as an incompetent lying sack of shit. The fuckwit just makes shit up, and flees in terror when people dare insist on evidence.

It's been awhile since I've read your blog, so, I was unaware that you still had anything to do with Dr. Jackson. If by chance you and he correspond with each other directly, tell him that Matt Hardison tells him and his 1970's -New York City -pornographer's mustache, "Hiiiiiiii!"
By the by, I shall screen e-mails from his pastor minion John Miller, a.k.a. the "Son of Thunder", a.k.a. "What the fuck is up with me being called the 'Son of Thunder'?"

So, I watched the debate on Youtube, and I watched the "unedited" version that you (Abbie) posted on this site. If there is such an animal, I am an agnostic. I'm open to the possibility that anything is possible. However, you (Abbie) seem to have been bested by this man Charles Jackson. I hope you don't take this the wrong way, but you seemed ill prepared for this event. Jackson at least could answer each question with something relevant, even if it was the old creationsist stuff. You on the other hand, insisted on talking about viruses as the only proof for your claims of evolution. There are better arguments to consider, and in this case, you failed to make your point. I hope in the future you spen more time preparing yourself for these types of events. Jackson never claimed to know everything, but how can you be so sure that an intelligent being didn't in some way assist the creation of this planet? At the end of the day, you still can't answer, and I doubt you ever will, where did all these viruses come from? When and how did it all begin? Let me know if you ever find an answer for that...

@The Texan:

The title of the debate was "Does Molecular Genetics Support Human Evolution?" Abbie talked about molecular genetics. Dr. Jackson pulled out dinosaur fossils in an attempt to date the earth to 6000 BC. Abbie is not a fossil expert, and he used this to try to convince the ignorant masses that he must be right. (I should point out, Abbie is/becoming an expert in ERVs, while Jackson is an expert in NO field of science, unless you want to count science mis-education.)

Abbie never claimed to know everything either. How can you be sure that an invisible pink unicorn didn't in some way assist the creation of this planet? A better question is, what do these lines of inquiry add to science? What predictions do they make? None whatsoever.

Tell me, what creation "scientist" was expecting to find evidence of fusion in human chromosome #2? Why would they even think to look for that? They wouldn't. It was predicted ONLY by the theory of evolution and common descent.

Abbie, I am surprised by your unprofessionalism. After watching the video, in which you came off as the âgreenâ graduate student that you are, I am totally turned off by your labeling of your fellow debater as a "fucking moron". This along with other arrogance pretty much discounts what little credibility that I have given you the benefit of. You should be more humble given your lack of presentation skills. Sorry to say but the Creationist in the video âownedâ you.

I hope that you learn from your immaturity especially if you would like to be taken seriously in the science profession.

charles jackson argues a croatian astrophysicists
http://www.youtube.com/watch?v=jqHNNpZyXt4&feature=player_embedded

I loved reading this blog. I really laughed at this part...

"Here's why they matter: To become inherited, an ERV must get into a sex cell." LOL!!

Here's why they matter: To become inherited, an ERV must get into a sex cell.

That's only a theory . . .