Posts by cognisonance

6

Huge Research Finding relates to the brochure: ORIGIN OF LIFE, THE—FIVE QUESTIONS WORTH ASKING

by cognisonance in

first the new finding: summary and the actual paper.. now, consider this snippet from that brochure, especially the bold emphasis i've added (pages 5-7):.

researchers have learned that for a cell to survive, at least three different types of complex molecules must work togetherdna (deoxyribonucleic acid), rna (ribonucleic acid), and proteins.

today, few scientists would assert that a complete living cell suddenly formed by chance from a mix of inanimate chemicals.

cognisonance

As regards probability calculations. I found this on TalkOrigins that might be helpful for people who don't have much probability background:

Coin tossing for beginners and macromolecular assembly

So let's play the creationist game and look at forming a peptide by random addition of amino acids. This certainly is not the way peptides formed on the early Earth, but it will be instructive.

I will use as an example the "self-replicating" peptide from the Ghadiri group mentioned above [7]. I could use other examples, such as the hexanucleotide self-replicator [10], the SunY self-replicator [24] or the RNA polymerase described by the Eckland group [12], but for historical continuity with creationist claims a small peptide is ideal. This peptide is 32 amino acids long with a sequence of RMKQLEEKVYELLSKVACLEYEVARLKKVGE and is an enzyme, a peptide ligase that makes a copy of itself from two 16 amino acid long subunits. It is also of a size and composition that is ideally suited to be formed by abiotic peptide synthesis. The fact that it is a self replicator is an added irony.

The probability of generating this in successive random trials is (1/20)^32 or 1 chance in 4.29 x 10^40. This is much, much more probable than the 1 in 2.04 x 10^390 of the standard creationist "generating carboxypeptidase by chance" scenario, but still seems absurdly low.

However, there is another side to these probability estimates, and it hinges on the fact that most of us don't have a feeling for statistics. When someone tells us that some event has a one in a million chance of occuring, many of us expect that one million trials must be undergone before the said event turns up, but this is wrong.

Here is a experiment you can do yourself: take a coin, flip it four times, write down the results, and then do it again. How many times would you think you had to repeat this procedure (trial) before you get 4 heads in a row?

Now the probability of 4 heads in a row is is (1/2)^4 or 1 chance in 16: do we have to do 16 trials to get 4 heads (HHHH)? No, in successive experiments I got 11, 10, 6, 16, 1, 5, and 3 trials before HHHH turned up. The figure 1 in 16 (or 1 in a million or 1 in 10^40) gives the likelihood of an event in a given trial, but doesn't say where it will occur in a series. You can flip HHHH on your very first trial (I did). Even at 1 chance in 4.29 x 10^40, a self-replicator could have turned up surprisingly early. But there is more.

1 chance in 4.29 x 10^40 is still orgulously, gobsmackingly unlikely; it's hard to cope with this number. Even with the argument above (you could get it on your very first trial) most people would say "surely it would still take more time than the Earth existed to make this replicator by random methods". Not really; in the above examples we were examining sequential trials, as if there was only one protein/DNA/proto-replicator being assembled per trial. In fact there would be billions of simultaneous trials as the billions of building block molecules interacted in the oceans, or on the thousands of kilometers of shorelines that could provide catalytic surfaces or templates [2,15].

Let's go back to our example with the coins. Say it takes a minute to toss the coins 4 times; to generate HHHH would take on average 8 minutes. Now get 16 friends, each with a coin, to all flip the coin simultaneously 4 times; the average time to generate HHHH is now 1 minute. Now try to flip 6 heads in a row; this has a probability of (1/2)^6 or 1 in 64. This would take half an hour on average, but go out and recruit 64 people, and you can flip it in a minute. If you want to flip a sequence with a chance of 1 in a billion, just recruit the population of China to flip coins for you, you will have that sequence in no time flat.

So, if on our prebiotic earth we have a billion peptides growing simultaneously, that reduces the time taken to generate our replicator significantly.

Okay, you are looking at that number again, 1 chance in 4.29 x 10^40, that's a big number, and although a billion starting molecules is a lot of molecules, could we ever get enough molecules to randomly assemble our first replicator in under half a billion years?

Yes, one kilogram of the amino acid arginine has 2.85 x 10^24 molecules in it (that's well over a billion billion); a tonne of arginine has 2.85 x 10^27 molecules. If you took a semi-trailer load of each amino acid and dumped it into a medium size lake, you would have enough molecules to generate our particular replicator in a few tens of years, given that you can make 55 amino acid long proteins in 1 to 2 weeks [14,16].

So how does this shape up with the prebiotic Earth? On the early Earth it is likely that the ocean had a volume of 1 x 10^24 litres. Given an amino acid concentration of 1 x 10^-6 M (a moderately dilute soup, see Chyba and Sagan 1992 [23]), then there are roughly 1 x 10^50 potential starting chains, so that a fair number of efficent peptide ligases (about 1 x 10^31) could be produced in a under a year, let alone a million years. The synthesis of primitive self-replicators could happen relatively rapidly, even given a probability of 1 chance in 4.29 x 10^40 (and remember, our replicator could be synthesized on the very first trial).

Assume that it takes a week to generate a sequence [14,16]. Then the Ghadiri ligase could be generated in one week, and any cytochrome C sequence could be generated in a bit over a million years (along with about half of all possible 101 peptide sequences, a large proportion of which will be functional proteins of some sort).

Although I have used the Ghadiri ligase as an example, as I mentioned above the same calculations can be performed for the SunY self replicator, or the Ekland RNA polymerase. I leave this as an exercise for the reader, but the general conclusion (you can make scads of the things in a short time) is the same for these oligonucleotides.

6

Huge Research Finding relates to the brochure: ORIGIN OF LIFE, THE—FIVE QUESTIONS WORTH ASKING

by cognisonance in

first the new finding: summary and the actual paper.. now, consider this snippet from that brochure, especially the bold emphasis i've added (pages 5-7):.

researchers have learned that for a cell to survive, at least three different types of complex molecules must work togetherdna (deoxyribonucleic acid), rna (ribonucleic acid), and proteins.

today, few scientists would assert that a complete living cell suddenly formed by chance from a mix of inanimate chemicals.

cognisonance

First the new finding: Summary and the actual paper.

Now, consider this snippet from that brochure, especially the bold emphasis I've added (pages 5-7):

Researchers have learned that for a cell to survive, at least three different types of complex molecules must work together—DNA (deoxyribonucleic acid), RNA (ribonucleic acid), and proteins. Today, few scientists would assert that a complete living cell suddenly formed by chance from a mix of inanimate chemicals. What, though, is the probability that RNA or proteins could form by chance?*

Many scientists feel that life could arise by chance because of an experiment first conducted in 1953. In that year, Stanley L. Miller was able to produce some amino acids, the chemical building blocks of proteins, by discharging electricity into a mixture of gases that was thought to represent the atmosphere of primitive earth. Since then, amino acids have also been found in a meteorite. Do these findings mean that all the basic building blocks of life could easily be produced by chance?

“Some writers,” says Robert Shapiro, professor emeritus of chemistry at New York University, “have presumed that all life’s building blocks could be formed with ease in Miller-type experiments and were present in meteorites. This is not the case.”2*

Consider the RNA molecule. It is constructed of smaller molecules called nucleotides. A nucleotide is a different molecule from an amino acid and is only slightly more complex. Shapiro says that “no nucleotides of any kind have been reported as products of spark-discharge experiments or in studies of meteorites.”3 He further states that the probability of a self-replicating RNA molecule randomly assembling from a pool of chemical building blocks “is so vanishingly small that its happening even once anywhere in the visible universe would count as a piece of exceptional good luck.”4

What about protein molecules? They can be made from as few as 50 or as many as several thousand amino acids bound together in a highly specific order. The average functional protein in a “simple” cell contains 200 amino acids. Even in those cells, there are thousands of different types of proteins. The probability that just one protein containing only 100 amino acids could ever randomly form on earth has been calculated to be about one chance in a million billion.

Researcher Hubert P. Yockey, who supports the teaching of evolution, goes further. He says: “It is impossible that the origin of life was ‘proteins first.’”5 RNA is required to make proteins, yet proteins are involved in the production of RNA. What if, despite the extremely small odds, both proteins and RNA molecules did appear by chance in the same place at the same time? How likely would it be for them to cooperate to form a self-replicating, self-sustaining type of life? “The probability of this happening by chance (given a random mixture of proteins and RNA) seems astronomically low,” says Dr. Carol Cleland*, a member of the National Aeronautics and Space Administration’s Astrobiology Institute. “Yet,” she continues, “most researchers seem to assume that if they can make sense of the independent production of proteins and RNA under natural primordial conditions, the coordination will somehow take care of itself.” Regarding the current theories of how these building blocks of life could have arisen by chance, she says: “None of them have provided us with a very satisfying story about how this happened.”6

Of course there are some semantic and red-herring issues when it comes to how JWs use the phrase "by chance" in their publications. Evolution isn't merely by chance, that's just half the, it's rather by the non-chance selection of chance mutations. For example the paper I've linked to even addressing this when talking about the odds of their finding happening by chance:

[E]ven if one were to deny all of these arguments and assert that our findings could be due to chance, chance does not obviate the observation that tRNA appear to be encoded in rRNA, that rRNA may have been the evolutionary source of tRNA or that tRNA may have, conversely, given to rRNA. Evolution works by chance. The issue is not whether the appearance of tRNA in rRNA is by chance, but whether there was selection for such chance events that has caused these homologies to be retained through evolution and we claim there was because of additional data we offer concerning the unusually high degree of active site protein modules associated with ribosome function that are also encoded in the rRNA.

Anyway, this new paper has some interesting tidbits among other more important things (such as putting forth the selfish ribosome model as opposed to selfish gene model). For example, when it comes to RNA molecules and Proteins cooperating for self-replication the paper says:

In short, two conclusions are inescapable. First, the ribosome-related information encoded in rRNA is extremely dense—so dense as to make it extremely likely that extensive selection over a very long geological period of time must have been at work to incorporate its many facets. rRNA appears to have been used evolutionarily as structural components of the ribosomes themselves; as tRNAs to translate the sequences; as mRNAs, using all possible reading frames, to encode key ribosomal proteins; and it is also highly redundant, encoding some functional elements such as tRNAs, polymerases and ligases in multiple ways. A second conclusion is that rRNA specifically encodes molecules associated with functions that could potentially have permitted a primitive ribosome to reproduce itself. The fact that all of this information resides in the ribosomes of present-day E. coli (and other bacterial) species must be considered in light of several billion years of evolution that have occurred since ribosomes were incorporated into cells. The remaining homologies are almost certainly vestigial and represent fragments remaining after gene loss or transfer to the cellular genome. Thus, the primordial ribosome may have been more complex or complete than that represented by our search strategy.
Another likely implication of our results is that RNA co-evolved with proteins to yield a self-organizing, self-replicating entity. Given the high information density found in the ribosome, selection is likely to have been for peptides that could bind to the RNA sequences encoding them (i.e., for molecular complementarity) and the resulting RNA-peptide interactions would additionally have been selected for their functions (ability to form platforms that bound other RNA sequences; promoted peptide formation; had RNA or DNA polymerase or ligase activity; stabilized RNA and/or peptides against degradation; etc.) (Hunding et al., 2006 and Root-Bernstein and Dillon, 1997). Prebiotic tRNAs, for example, may not have been just tRNAs, but also mRNAs that encoded crucial peptide sequences with various enzyme or structural functions that were enhanced by binding to their own, or other tRNA sequences. Specialization of RNA into ribosomal, messenger and transfer types likely came later in evolution.

3

How good are we at spotting propaganda and logic fallacies outside the religion of the JWs?

by cognisonance in

jw
friends

in the book take back your life, recovering from cults and abusive relationships, i think it mentioned that many often jump from one cult (or abusive relationship) to another, not being able to see the tell-tale signs with foresight, only hindsight.

therefore, i encourage everyone to take at least a cursory look at this report.

what are your thoughts?.

cognisonance

In the book Take Back Your Life, Recovering From Cults and Abusive Relationships, I think it mentioned that many often jump from one cult (or abusive relationship) to another, not being able to see the tell-tale signs with foresight, only hindsight. Therefore, I encourage everyone to take at least a cursory look at this report. What are your thoughts?

Additionally, the following article may be interesting as well, precisely for not being propaganda: The Nightmare in Gaza.

43

Update to Rio Rancho, NM Kingdom Hall

by Newly Enlightened in

https://www.facebook.com/photo.php?fbid=678180165590951&set=o.585807931515647&type=1.

.

cognisonance

Looks like he's made a sign?

https://www.facebook.com/photo.php?fbid=661717067237261&set=o.585807931515647&type=1&permPage=1

16

Update on shunning@the store. Watchtower victorious.

by quellycatface in

jw
friends

yep, that's right.

after all my friends and my efforts, the shunning carries on.. the 3 people who were shunning me at my local supermarket, still, are carrying on this practice.. little subtleties like avoiding eye contact, making busy as i walk past and looks out of the corner of their eyes.

you know the modus operandi.. nothing now the store can do about it.

cognisonance

Fair enough. It is sadly ironic as you say. I really feel sorry for the friends that left me behind when I decided to never return to their religion.

16

Update on shunning@the store. Watchtower victorious.

by quellycatface in

jw
friends

yep, that's right.

after all my friends and my efforts, the shunning carries on.. the 3 people who were shunning me at my local supermarket, still, are carrying on this practice.. little subtleties like avoiding eye contact, making busy as i walk past and looks out of the corner of their eyes.

you know the modus operandi.. nothing now the store can do about it.

cognisonance

It's sadly ironic. JWs give a lot of lip-service to being "courageous" and "standing-firm for righteousness," but the truth is they all succumb to fear of manwhen they are blindly obedient to the capricious dictates of the WTBTS, their golden idol.

That may be what is happening, but for the true believer, I doubt they are aware of that. They really think they are obeying god. They don't realize they are succumbing to fear of man. They may be blindly obedient, but it's becase their minds are controled and don't see what is really happening. They are captives to the religion.

16

Update on shunning@the store. Watchtower victorious.

by quellycatface in

jw
friends

yep, that's right.

after all my friends and my efforts, the shunning carries on.. the 3 people who were shunning me at my local supermarket, still, are carrying on this practice.. little subtleties like avoiding eye contact, making busy as i walk past and looks out of the corner of their eyes.

you know the modus operandi.. nothing now the store can do about it.

cognisonance

If people choose to act like that do you really want to interact with them anyway? I don't, I'm happy enough without having to make small talk with such people

The problem is, if they are true believers, they really don't have a choice do they? Certain people shun me and the few times I did get to speak with them they told me that they don't want to but they have to be loyal to thier god... It's not really a choice when they really believe god is holding a gun to their head if they talk to former believers is it?

76

Do You Like or Dislike Algebra? Why and Why not?

by Scott77 in

july 28, 2012is algebra necessary?by andrew hacker .

a typical american school day finds some six million high school students and two million college freshmen struggling with algebra.

in both high school and college, all too many students are expected to fail.

cognisonance

I will give when it comes to tackling the algebraic aspects of calculus is one I emphasize again and again to my students: TAKE YOUR TIME!!! Many mistakes can be eliminated by not being in a hurry to solve a problem. Also, look over the test when you get it and do the easy problems first. That will leave you a lot of time to pore over the more challenging ones and you won't feel yourself under as much pressure.

I tried doing this on my last exam (taking my time). I wasn't rushed, but I only had enough time to try each problem once without any time to double check. I felt goo about the test (and I actually did well on the previous quizs for the chapter gettings a 70, 100, 95, and 100). I thought I was going to get a high B, low A. My score? 81.5% after a curve (76.5 originally). The professor told us curves will be rare, so don't rely on them, even though both exams have been curved so far. I haven't gotten my test back yet even though I took it almost 2 weeks ago. We have two teacher teaching this class as they are dealing with vacation this summer and the teacher that gave us the last exam is now on vacation, but mailed the tests to the other teacher. I should have them tomorrow. My grades are online so I can at least see how I'm doing. In other exam where I went faster, I had time to double check my work. Either way it doesn't make much difference (that test grade: 70%, after curve 80%). The mistakes from going fast with double checking (and thus fixing some mistakes), are about the same as the mistakes from going slow without.

I've always been a slow test taker in high school and college from over 10 years ago, and the same is true today. I'm the type of student that thinks really deeply about problems and typically spends on average, about 15 minutes a problem on calc 1 homework (which makes this take a long time, as I usually have about 50 problems to do each week). I do practice some problems before an exam to make sure I can solve them in say around 4 minutes, but it's always difficult. I'm just not fast, even if I understand the concepts and how to do things.

I'm not a fast reader (even though I've bought a speed reading book and have tried to increse it, around 160-200 words/minute deepending on the material). I'm a softare engineer, and when I program, I'm also a slow thinker and want to fully understand what I'm about to do before I just jump in and get stuff done, but the quality of my work is very high.

Essentially, If I had say, 2-3x the time that is typically devoted for a Calculus exam or test, I'm sure my grade would be a solid A, not hovering around the C/B range. If I go slowish on a test (that is only time to attempt each problem but not double check) it's still fast for me. I get to the answer and can tell it's not right, but have no time to fix it. If I try going faster, then I just make even more mistakes, and while I have some time to fix them, it just seems to be a wash with when I go a bit slower. I just am a student that needs more time!!! I try to devote more time to studying, but this is difficult working full time even though this is the only class I'm taking this summer. I'm spending about 15-20 a week on homework. And another 5-10 hours a week on supplimental review, quiz, and exam prep. So 40-hours of working, plus 20-25 hours of school. I don't really know how to devote even more time to become faster.

I've also bought 3 supplimental books (humungous book of calculus problems, calculus lifesaver, and pre-calc for dummies). I only really have time for the pre-calc book for review looking up something I have forgotten (like the unit circle or factoring polynomials). I also use Khan academy to practice those concepts. I have test taking anxiety, which after 2 exams and a dozen quizes I'm just beginning to learn to deal with. As mentioned I'm a slow test taker. The classes are in the evenings after a long day of work, and my study time is mostly in the evenings as well. The best time for me is in the mornings to have my mental capacities running at optimum, but I work most of the time. I only have the weekend to work on class in the morning. I'm making sure I get 8-9 hours of sleep each night. I'm eating healthy. I take breaks when I get stuck on problems in the homework, but I am a bit stuborn in that I won't skip then until I finish them.

I'm trying my best and I'm struggling to get a B- in this class. I never in my life struggled this hard with any class, including math (though I've always struggled somewhat with math but chaulked this up in the past to not really trying hard [because I feel I didn't try as hard as I could or really do my homework like I should]). This time around I'm giving in all the time I have. All the focus I can. I'm thinking about math so much that I often dream about equations most nights. It's all consuming and I still just can't get anything higher than a B- on tests. And quizes hover in the 60-100% range, averaging around 80%.

I'm just frustrated!

76

Do You Like or Dislike Algebra? Why and Why not?

by Scott77 in

july 28, 2012is algebra necessary?by andrew hacker .

a typical american school day finds some six million high school students and two million college freshmen struggling with algebra.

in both high school and college, all too many students are expected to fail.

cognisonance

I'm taking Calculus right now. . . .

And you would think where I'd get hung up is in all that fancy calc stuff like derivatives, and derivatives of derivatives . . ..

But nooooooo. . . . . . all of those concepts I've got down pat.

Where do I always screw up? In the friggin algebra!

Drives me absolutely mad!

Same here! It's very annoying. My last test, where I thought I did really well (High B, Low A) turned out to be a low B (after a curve at that). I haven't gotten it back yet, but I suspect this is because of algebra mistakes. For me the issue with algebra is making small mistakes and not having enough time on exams to find the problems and fix them as in this last one, we had about 3.8 minutes a problem to solve and the bulk of the test is about Calculus concepts and algebra keeps getting in my way (and now the unit circle is beginning to as well).

20

Shunning at the Jehovah's Witness Convention San Diego 2014

by Watchtower-Free in

found this on youtube.

its interesting how jws act .creepy.

https://www.youtube.com/watch?v=eln4czqcul4&feature=youtu.be.

cognisonance

I agree with designs, when watching this I wondered what would be the reaction of people if he did this randomly to people on a busy street in a city and asked a simple question (for that audience), something like, "What city are we in." The fact he is filming and with a microphone would make many probably avoid him just like many do a pan handler on the streets. They probably don't want to be bothered, be recorded, etc.

I remember attending a convention in the 1990s, where I think were ex-members were outside protesting (and lot's of them). Hundreds of convention volunteers (elders?) went outside early after the convention to form a human barrier between the leaving delegates and the “apostates.” IIRC, those forming the barrier even locked arms or held a rope to prevent anyone from approaching the protestors, or the protestors approaching the leaving delegates. Having that on YouTube would be better at shoulding how much the religion is a cult. This video, not so much.