Thursday, May 31, 2012

My Apologies

Just a really quick post before I have to be off, again.

I've been neglecting you a little bit, and I'm very sorry. I have been crazy busy at work, I have deadlines screaming at me to pay attention to them and sometimes I fall asleep in front of my computer. I am trying to do better, and soon those deadlines will be behind me and I can update a little more regularly. In the meantime please accept my apologies, and I will try to update as often as I can.

In the meantime, feel free to ask me a question if there is something in particular that you would like me to address. Although I do not have very much time to address issues that involve a decent amount of research (I have a post on vaccines in the works that will take me a while to get back to) I can definitely cover one-paper questions, basic science or general ponderings with my current work load.

Anyway, thank you all for reading and commenting here, I appreciate your input, your thoughts and your readership.

Guys, There Is Such A Thing As Too Much LSD

I get a few videos sent my way on my youtube channel, usually they are music videos, occasionally there are a couple of questions about my thoughts on a particular scientific or political topic, but one of my first subscribers has taken to sending me his, um, spiritual training videos. Now I am fully aware that he is spamming thousands with them in the hopes of getting as many people as possible to pay for his program, but yesterday I actually found twenty spare minutes in my day to finally take a look at one of them. After all, my interest was piqued with the title "How To Have A Metamorphosis Of Your DNA!" as part of a series of videos involving "Superhero Training". This should be fun.

I was expecting to be far more amused and far less annoyed. A part from the weird dude in the blue pajamas at the beginning, the grating pronunciations of  the words "lychee" and "metamorphosis", and the random pig that just appears out of nowhere (that one at least was a little cute), I was surprised at just how incoherent these two are. I was expecting some semblance of an argument, albeit a ridiculous and scientifically ignorant one, but this was just amazing.

If unlike me you do not have twenty minutes to spare to watch the whole thing for yourself, let me transcribe one of my favorite incoherent ramblings:

So, you know, I look at myself today 'cause we're all like sort of becoming our own hero, because you have such underdeveloped DNA potential that you couldn't imagine, remember you're only two, strands activated like having a car that has twelve cylinders let's say or a lot of cylinders and you only have two activated now wouldn't you be sort of curious to see how it would run on maybe two and a half cylinders, or maybe three? And what would you have to do to do that? Mmha, a lot of different upgrades, or what we call terrain modifications, that we sort of have been playing with for many years and you've been playing with a lot of the terrain modification for this thing up here, the supercomputer, and I've been doing it for this little machine also called the, the dream machine, yeah, we dream this thing and actually it does what we want to at light speed and of course, you don't know how to do this do you? (opening and closing his hands) Do it. Try it. You open your hands in and out, only to dream this motion behind the scenes thousands and thousands of reactions are going along circulating your blood as I focus my eyes, as I hold my urine, as I do nothing, because this realm we're talking about, the realm that he's talking about here is sort of like the invisible realm or the mythological realm or the realm that maybe we don't "preceive" as real. 

My head hurts, mostly because that facepalm was a little too hard.

Of course they follow up by saying that scientists are telling us all how to make "microadjustments" to our DNA by thinking them into existence. I'm sure that you all know that it is a bunch of made up crap. There's no point in me pointing out that the double-stranded helix is simply referring to the structure of DNA and that there are actually billions of copies in our bodies, where they are all partially activated, and that there are no "other strands" to "activate" just waiting around, and that DNA is not the energy power source of our bodies, etc. etc. 

I was expecting to respond to a little amusing pseudoscientific tinkering, but this far beyond response. The most shocking part is it only has 3/42 dislikes, and most of the comments are from people who actually think these two are speaking wisdom, let alone capable of forming a coherent and grammatically correct sentence. Do they filter the comments section? Or perhaps they're not spamming as many people as I thought with their videos, but maybe subscribed to me and send me them because they saw videos of mine with titles like "Alternative Medicine" not realizing they are bullshit? Or do more people than I want to believe actually buy this crap?

Incidentally I do know quite a few people that are into this New Age-y crap, but none of them are this bad at explaining themselves. The ones I know are relatively intelligent people, if scientifically illiterate, overly empathetic and quite gullible. In fact the only person I know that comes close to this level of incoherency is my one friend who did far, far too much LSD in her life.

So guys, I'm sorry to say I think you've wrecked your heads quite permanently. I hope the effects are reversible, but you should probably stop doing those drugs now. If it's been a few years since your blow-out days, then I'm afraid you're stuck with the damage. 

Just please take me off the mailing list, I don't get any amusement out of it.

Sunday, May 27, 2012

How About A Litte Good Science?

Homosexuality and it's evolution has been a topic that has intrigued me ever since I attended a lecture on the subject during my third year in college. It is a dynamic and fascinating field and one that is too often oversimplified and overlooked, especially by those who refuse to accept it. I think that potholder54 did a very good job summarizing people's issues with it and the science behind it, and I wanted to share it here.

I have that book that Ricky Gervais is talking about, and it is very good. However, for a book that is more about the evolutionary theory (rather than a huge collection of examples) an excellent book is Evolution's Rainbow: Diversity, Gender and Sexuality in Nature and People by Joan Roughgarden. I don't 100% agree with absolutely everything she says, but it does bring a great perspective on a topic that is far more complex than we ever could have imagined.

Thursday, May 24, 2012

Book Review: The Hunger Games

OK, I am aware that I am totally late to this party. I know this book has had an enormous success in the United States and the movie had an even bigger one, but since in Italy no one has been talking about it at all I wouldn't even have known it existed if not for TheYoungTurks talking about it. Curious, I bought a copy.

I started reading it at 6AM on the train on my way back from Rome. By 6PM I had read the last page, sneaking pages between washes of my western blot (if you don't know what that is don't worry, it's not interesting at all). I just couldn't put it down, and those few times that I was forced to I couldn't stop thinking about it.

I'm sure you all know the story by now, and if you're a European like me and you don't I suggest you get a copy and see for yourself. Suzanne Collins has this amazing way of transmitting how, despite the dire disgusting social structure that the main characters have to live in, it has become everyday life while you choke down your occasional flares of indignation. It's unjust, it's inhumane, it's sickening, but it's her life, and you believe it. After all, it's not like there is no precedent. The Colosseum, public executions with crowds screaming for blood, human nature has the capacity to turn so feral that this book has a way of haunting your thoughts, that although you tell yourself that such a society could never arise again, you can't actually be sure of that. 

The build-up to the actual games is a mirror of our celebrity-venerating culture in how the "contestants" are fawned over and their every movement choreographed with their marketing in mind. However, there is always this terribly dark undertone, that once in a while you realize this is crazy! They're setting up to kill each other! The injustice of it made my blood boil, trying to imagine what would go through my head if I would be put in such a situation. Imagine if your brother or sister was called up with you, and you are forced to kill or be killed. Imagine being on the other side of the screen, and it being culturally acceptable to wait all year in anticipation for the time when you get to watch children murder each other for your entertainment. It is sickening, and yet not completely outside the realm of possibility, which makes it so much worse. 

Throughout the book I kept thinking, what if the two that were left made a pact and just refused to kill each other? What if they just sat in front of one another, not having any intention to participate in this disgusting game. Could that happen? It brings up the old Prisoner's Dilemma, how can you really trust the other person to not kill you first?

Which of course begs the question, which would you rather be? Would you rather be the martyr, or the traitor?

Wednesday, May 23, 2012

Ooh! A (Very, Very Long) Response...

So remember that post I wrote answering a creationist’s questions about abiogenesis? I got three PMs in response, which was actually quite surprising since they usually spam me with copy and pasted questions and then scamper off when I respond. However, as I said I will answer any question that is asked of me to the best of my abilities, regardless of whether or not I think they won’t reply, and in this case he did. Well, let’s take a look shall we?

Well, I got the answer I get from virtually every atheist or evolutionist I encounter. They say evolution has nothing to do with abiogenesis and that you can believe in evolution without having to worry about deciding where life came from. There is a huge problem here. First of all, you are overlooking the obvious fact that evolution is directly linked with abiogenesis. If there is no life, we cannot evolve from anything. If life cannot come from nonliving material, evolution is not possible. If there is no God, obviously life HAD to come into existence by itself andit HAD to be from nonliving material. Your argument that evolution has nothing to do with abiogenesis is simply incorrect.

All of the fields of biology and even science are linked in some way, that does not mean that evidence for (or lack thereof) of one discipline means that the other is false. By the same rationale you could say well the theory of evolution is directly linked with the theory of gravity, because without gravity all life would fall off the planet and float around in space, so any problems found with the theory of gravity mean evolution is a lie! Modern medicine is directly linked with evolution because without evolution there would be no vaccine development or reason to test drugs on animals, I don’t believe in evolution therefore I won’t go to the doctor! Just because the fields of science are interconnected does not mean that the evidence for them is in the way you are suggesting.

Now, onto your next attempt at answering my questions. You gave me details about a peptide being created and attempted to pass that off as life. I truly hope you were joking or maybe you were not thinking clearly because this is the most ridiculous answer I have ever gotten.If you want a more specific definition of life, how about this? A single-celled organism. Tell me where a single-celled organism has arisen in a lab from nonliving material. THAT is life. Do not give me the details about a peptide being created. That is completely ridiculous.

I am not trying to “pass” anything off as anything, I was giving an example of something that could conceivably represent a step between non-living and life, while illustrating that defining life is very difficult. Don’t the pro-lifers constantly say that IVF technicians are “creating life” every time they combine sperm and egg?

 So your definition of life is something that has a cell wall? Ham Smith and Clyde Hutchinson made a self-replicating bacteria in May 2010 at the J. Craig Venter Institute in San Diego, by chemically making its genome in the lab after having designed it in a computer. My guess is that is not going to be enough either, and you’ll change the definition of life again. The point I still don’t understand is why you are so hung up on scientists creating life as the ultimate proof of abiogenesis. Even if scientists created a frog in the lab from scratch, one that is in every way indistinguishable from a frog born from frogspawn, what would that matter? That would be nothing more than a pointless, extremely expensive endeavour, not proving or providing any evidence for abiogenesis. Ironically, the example of the self-replicating peptide is far more interesting in the scope of abiogenesis than making an animal in a lab is, but you dismiss it as “ridiculous”, which leads me to believe you actually don’t read up much on the evidence for abiogenesis as you previously claimed.

A peptide is a molecule consisting of 2 or more amino acids. Peptides are smaller than proteins, which are also chains of amino acids. Molecules small enough to be synthesized from the constituent amino acids are, by convention, called peptides rather than proteins. The dividing line is at about 50 amino acids. Depending on the number of amino acids, peptides are called dipeptides, tripeptides, tetrapeptides, and so on. These are some of the components that make up living organisms, however they are not living organisms themselves. Many experiments have been conducted attempting to create life from nonliving material using these "ingredients of life". However, they have all failed. They have even used conditions that are unrealistic in the natural world in an attmept to create living organsims. In more simplistic terminology, they were cheating in an attempt to create any sort of living organism. Sadly, even though they were using unrealistic conditions that were in their favor, they stil cannot create life.

Could you please provide your sources? What poor scientists were desperately trying to create life in an attempt to provide evidence for abiogenesis?

 I am feeling generous today, I will give you another chance to answer my question. Also, you say since scientists cannot create life, it is unreasonable to automatically assume "God did it". I am not saying it automatically proves that God did it. What I am saying is that the fact that we cannot create life is CONSISTENT with biblical scripture. It is NOT CONSISTENT with evolutionary/abiogenesis teaching. If life arose from nonliving material completely by chance, we should be able to replicate that process. However, we cannot. If God made life, we should not able to replicate that process. And guess what? We cannot create life.

Might I point out that a scientist actively creating something alive in the lab is not life “arising by chance” and therefore would still not provide the evidence that you are so desperately looking for?

And how is this consistent with biblical scripture? Does the bible say that humans will not be able to create life? And even if it did, what about all of the things that are in scripture like classifying bats as birds  or a man being able to live to see his 800th birthday, which are completely inconsistent with reality? What do those parts of the bible say to its veracity and unerring nature?

Also, in response to your attempt at answering my quetion, you gave me a false answer about the peptide being created in 1996.
Here is a quote from the website detailing your findings:

(It wouldn't let my copy and paste, but feel free to google this statement. I copied it word for word from the article detailing the 1996 experiment you discussed.)

"Because the peptide with 32 amino acids facilitates the formation of this single peptide bond, Lee claims that this peptide can self-replicate. But is this really true? To self-replicate, this peptide requires a pool of two peptides. One of these peptides has the same amino acid sequence as the first 15 amino acids in the self-replicating peptide, and the other has the amino acid sequence as the next 17 amino acids. Where do these peptides come from? In this case, they are supplied by the investigator."

Did you forget to mention that part? I think you did. Wow- scientists cannot even create self-replicating peptides from nonliving material. That is pretty sad. 

I did google it and guess what? It comes from a creationist website (of course). Not including what a creationist had to say is not forgetting, it’s omitting irrelevant information. However the fact that a creationist found Lee et al’s work to be important enough to try to butcher on their website should be an indication that it is not as “ridiculous” work as you think. If you want the real information the paper is free, which is one of the reasons I picked it, you can find it and read it yourself here 

As for you saying no scientist would say that E.Coli or anything similar to that would suddenly pop out of the ground, I completely agree with you. However, the bottom line is that there are NO examples of life coming from nonliving material in nature (The Law of Biogenesis) and we cannot create life from nonliving material in a lab.

The Law of Biogenesis, as in Pasteur circa 1860? I agree with him that spontaneous generation is not correct, but we really have come quite a way in science in the past century and a half. 

After 24 hours, I got this amusing little follow-up

You completely ignored my statements. You refused to admit that I proved scientists could not create the peptide you claimed and that your attempts at debating me have failed in every respect. You refuse to see the evidence and stubbornly hold on to nothing to support your ridiculous claims. You didn't reply to any of my arguments. You are truly pathetic.

Honey, when you have two jobs, deadlines coming up, squeezing in travel time and being a part-time youtuber and blogger, not getting back to you within a day is not called “ignoring [your] statements”, it’s called “being busy” (or “having a life”, if I want to be snarky about it).

So since you obviously have far more time on your hands than I do, why don’t you state your position a little more clearly (as well as providing the sources I asked for earlier):

1     1. What properties exactly does a bacteria possess that a self-replicating peptide does not that qualifies it as life?

         2. Why do you think creating a single-celled organism from scratch in a lab would disprove creationism and prove abiogenesis?

3  3.  How do you explain scripture that is blatantly inconsistent with reality? If your answer is “those parts are not literal”, then how do you objectively discriminate between what parts to take literally and which parts not to? If your answer is “back then those things were true/worked, they just aren’t/can’t now” then what evidence do you have of that? Has anyone been able to reproduce those ancient conditions in a lab and confirm what the bible says? (If not, by your logic, there’s a problem…)

And finally, and most importantly

        4. If you were to encounter the scientific experiment you seek, that fit all of your criteria unequivocally, would you begin to doubt creationism?

Think about that last one, because if the answer is no, there is absolutely no point in continuing to educate yourself in science or pestering scientists with questions you don’t want the answers to.

Unless you particularly enjoy building straw men and then beating them to death.

***EDITED TO ADD: I got a response back again from this guy. Apparently, pointing out that he's hanging his hat on a straw man is actually "admitting that [I'm] losing the debate". He didn't answer the questions, a part from saying that he would doubt creationism only if scientists created multi-cellular organisms every day in the lab (*facepalm*), did not address the fact that bacteria have been made repeatedly, and declared the "debate" over. As per my rule he has not responded with any new or relevant points, facts or opinions, so there goes another on the growing pile.

Tuesday, May 22, 2012

Book Review: Survivor

I managed to squeeze another little weekend to Rome, and my first book accompanying me on the way down was Chuck Palahniuk's Survivor.

If you've never read any of Palahniuk's books before, a warning is in order, the tone is incredibly nihilistic and his main characters tend to be fairly misogynistic, not as bad as Ian M. Banks' The Wasp Factory, but in the same league. If you are going through a depressing time in your life, not feeling like it's really worth living or just bored to death with society at large you should definitely wait before reading this book, unless you're the type of person that feels better about their own lives when reading about the misery of others.

Survivor starts at the end, with a man on a flight he has just hijacked (although it is now completely empty, including the pilot) and he wants to record his story in the black box so that it will be found after the plane crashes, so that he has a chance to explain himself and his actions. The entire book is his story, what his childhood was and how he ended up committing suicide by hijacking a plane. Even the chapters and the pages count backwards, which may not sound like much, but it really adds a finality to the story that makes you anxious, realizing that you only have 40 pages to go, or you've reached chapter 1.

In classic Palahnuik style the book is a grossly exaggerated satire on today's Western culture, what we value, what we are willing to believe and what image we will buy in to with the right marketing. Although he definitely has a point his incredibly nihilistic way of delivering it makes sure you're not laughing (unless you are the most cynical person I know), and you have to make sure you are able to take a step back and understand that it is still satire, without getting to depressed about the direction our culture is taking.

So what gives, did I like it or not? I can't really say for sure, because I'm always so torn with Palahniuk's books. I acknowledge that he is an amazingly gifted writer. I concede that his overall message is valid and that he has a very original way of saying what he has to say. I never walk away from his books with a real smile on my face, but rather an expression of shock, which is why I suppose I refrain from giving them my all out praise.

But I keep coming back to his books, which means I must like them, I just haven't put my finger on why yet.

Friday, May 18, 2012

Thoughts On: Logic and Its Bad Rep

After I was attacked about this for the third time, I wanted to take a minute to really think about why such different people would use the exact same language in berating me for being, in their words, “too logical”.

The discussion often begins with my expressing my frustration with people that are illogical. By this I mean people who either A) Believe in something because they want to, or like the sound of it, regardless of whether or not they have any other reason to; B) Will not change their opinion about something despite evidence to the contrary, or C) Prejudge what they like or dislike before having any facts or experience to base their ideas on (this one can range from racists assuming someone is a bad person to picky eaters refusing to try something they already “know” they’ll dislike). This follows with me priding myself in being what I think is a logical person. I try to be as objective in my reasoning as possible, and when I come to a conclusion it is based on the facts presented to me at the time, and that conclusion, once reached, will not change unless I find new contradictory evidence or I find a flaw in my original reasoning process. I will never understand people who are completely convinced one way one day and the next manage to pretzel-think themselves into the complete opposite opinion, nothing else having changed.

When the conversation gets to this point, I always get scoffed at. Despite three different people having had this conversation with me, at least one of which I find to be a very rational person (she is on her way to becoming a scientist after all) said the same thing. “Well, you can’t be too logical! That’s not good either! Being too logical leads to just as limited a life as being illogical.” I always respond “OK, why?” Answer: “Um…. you know…. it just does….. you can’t just live life based on logic…” but no good example has ever been presented. I counter argue this lack of argument saying that I don’t think it is limiting at all, and if you have a good example of how it is please share it.

First of all, taking on a common misconception. By being “logical” I do not mean denying the existence of emotion. By being “logical” I do not mean lacking empathy. By being “logical” I do not mean not ever having a “bad feeling” about something, or a “good feeling” about something without being able to explain what made you feel that way.  Let’s take a look at a couple dictionary definitions:

Logical: reasoning in accordance with the principles of logic,  as a person or the mind

1. the science that investigates the principles governing correct or reliable inference.
2. a particular method of reasoning or argumentation: We were unable to follow his logic.
3. the system or principles of reasoning applicable to any branch of knowledge or study.

Reasoning: the process of forming conclusions, judgments, or inferences from facts or premises.

There it is, inferences from facts or premises.

When I say “logical”, I mean that if there is direct evidence to contradict that feeling, and/or you find that the source of it is not something that should make you feel frightened (for example you had a bad dream with a lot of red in it and then you walk into a red room and get that frightened gut feeling because of it) that you are able to get over your irrational fear. I mean that you are willing and able to change your mind about something when you are presented with evidence that goes contrary to your belief, despite how unpalatable you find the alternative. To me this is being truly open-minded: to be willing to believe in anything so long as there is evidence for it. I mean the exact opposite of what I previously listed as traits of the illogical.

The fact of the matter is, “logic” and “rationality” just have a bad rep. None of these people I was by now having a one-sided argument with could give me any good reason as to why they rejected the terms, they just rang as “bad thing” in their heads. Why is that? Why do these things have such a bad reputation?

Is it a lingering influence of organized religion in our society and in the backs of our minds? Even though one of the aforementioned people is and atheist, one a pantheist and the other a deist at best, could it still be that organized religion has left its taint on them in this way? Why else is there this visceral distrust of reasoning, using one’s brain to sceptically question and seek the truth? What else thrives on people not encouraged to base their opinions on facts? Dictatorships probably, but none of us grew up in one.

What do you think? When I initially talked about being a logical person, did you also instinctively balk at the word? Why do you think that is?

Thursday, May 17, 2012

What Do You Mean By "Life"?

As an outspoken atheist and science-freak I often get asked some pretty standard questions about the more shall we say “controversial topics” in science. Some of them I cannot answer, some only in part, but many are so often repeated that I have decided to make blogposts out of the ones where I wind up having to repeat myself. This morning I got one such PM about abiogenesis, and since it is a pretty standard version of the questions I get about this topic I figured I’d post it here with my reply – a handy link to this post will save me time in the future.

Subject: Evolution

Well here we have our first problem. As I’m sure many of you have already heard, evolution is not a theory about the origins of life. Evolution explains the diversity of life as we see it today; it makes no speculation about how the very first living organism began. This may seem like splitting hairs for some, but it is fundamentally important.

You can believe in the theory of evolution without believing in the theory of abiogenesis, and I know far more people that choose this as their belief system than I know people who deny both. You can believe that the lighting that struck the primordial soup was God’s finger to zap together those first little building blocks of life, without denying a single piece of evidence that supports the theory of evolution. Even if scientists find a way to create a multicellular organism from nonliving compounds in a lab you can still believe that that’s not what actually happened all those billions of years ago. I’m not saying I agree or that it is particularly logical, but alas to each their own opinion.

I have a question for you. You obviously do not believe in God so I was wondering if you could help me out with something I have been wondering. Since life had to begin by chance from nonliving material I would like you to give me a SPECIFIC EXAMPLE of a living organism created ENTIRELY FROM NONLIVING MATERIAL in a lab, controlled environment, etc. ( I assume you know the difference between creating life from nonliving material and genetic engineering/bioengineering since genetic engineering and bioengineering are processes that deal with naturally occurring cells found in nature as well as DNA. Obviously this is not creating life from nonliving material.)

Well here we have another problem. What does God have to do with any of this? It is a common misconception that science exists to prove or disprove God, or that science has anything to do with the supernatural. If God is supernatural then by definition he (She? It.) lives outside of the natural world, and therefore cannot be tested for by natural means. Science involved testing the natural world, the two cannot be further apart.

Secondly, I do not like the “God of the gaps” fallacy that this question is implying. The argument “you can’t explain that! Therefore God” has no basis in logic or reasoning and you should all know this. It is a giant cop-out, and an arrogant way of implying that we as a species have learned everything that there is to know. The real statement to make about such things is “you can’t explain that yet”. Where would we be as a species if we were content with just “Goddidit” or “Devildidit”? Modern medicine, among other things would not exist.

I also spot a little misinterpretation of abiogenesis theory with “life had to begin by chance”, but he does not elaborate on the faux creationist probability argument so I’ll let it go as a slip up for now.

On to the question at hand. He wants a specific example of a living organism created by scientists, I’ll let him elaborate (and since genetic engineering is pretty much what I do yes, I know the difference between creating life and altering it).

Several examples of scientists who work with synthetic engineering and bioengineering are Dr. Venter and Dr. Szostak and multiple others.

They have admitted what they are doing is not creating life from nonliving material. The process of life coming from nonliving material is called abiogenesis so I want you give me a specific example of abiogenesis that has been successfully done in a lab by scientists. Since according to atheists life came into existence completely by chance billions of years ago, surely we can create life from nonliving material as well. So here is what I want you to give me IN SPECIFIC DETAIL:

1. The name of the organism that was created by scientists.
2. The location of the lab it was created in.
3. The name of the scientists who created it completely from nonliving material.
4. The year in which life was created by these scientists.

Well here we have to fix the goalpost from shifting with a simple question: What exactly do you mean by life? No scientist will tell you that a complex cellular organism popped up from nonliving materials in a single step: only creationists believe that complex organisms rose from nonliving material (In Genesis God makes Adam from clay, does he not?). Complex organisms came about after billions of years of evolution involving multiple steps that can be traced back to eventually a nonliving material. So at what point to we say this step is still nonliving, whereas the step right after can be called alive? It is a question that even scientists vehemently fight over. However, there are three criteria that are essential to calling something “alive”:

  1. It has to be able to make copies of itself, either directly or by placing itself in such a way so as to take advantage of something else’s replicating machinery
  2. Those copies have to resemble the original, meaning that the peculiarities of the original have to be “inherited” by its copies (although the copies need not be perfect)
  3. Those copies also have to be able to replicate, as per criteria 1.

Those are the criteria that are indisputable, and whether or not to tack on more is something fought over. If you wish to bring up other criteria to tack on there we can certainly have a follow up of this debate.

Anyway, what evidence do we have of this so far? Well, a specific example could be the self-replicating peptide created in 1996. So let’s give him what he asked for:

  1. Name: alpha-helical peptide based on the leucine-zipper domain of GCN4
  2. Location: La Scripps Institute, La Jolla, California.
  3. Scientists: David H. Lee, Juan R. Granja, Jose A. Martinez, Kay Severin, M. Reza Ghadiri.
  4. Year: 1996

I’m guessing a self-replicating peptide is not going to be good enough for this person. However, before firing back with “a molecule is not alive! Give me LIFE!” please include a very clear definition of what you consider “life” to be. Also, please note that no scientist claims a fully functioning E. coli just popped out of the mud.

If you cannot answer these questions, there is a huge problem we have here. If life cannot come from nonliving material, there would be no life on the planet. So hopefully, you can give me these answers in very specific detail otherwise the idea that life can come from nonliving material is in serious trouble.

Again with this fallacy. Just because something has not been done in a lab does not mean that it cannot be explained. You cannot hold a star in your lab and watch it die, but astrophysicists can tell you what happens when one does. Even if you can’t do it in a lab because you don’t have an explanation does not mean that an explanation does not exist or is impossible. New things are discovered all the time, it is one of the wonders of humanity. 

Also, do not bother giving me THEORIES as to how life could have arrived here. I love reading those, I have read many of those, but I am looking for actual experimental results. I am not interested in theories that have never been proven. So, please, do yourself a favor and give me specific details about actual experimental results, not theories, because if you give me theories about how life could have come into existence on Earth by itself billions of years ago by chance from nonliving material, surely we can create life from nonliving material as well. Remember, no theories, just RESULTS. Thank you.

Well good, that saves me the time of looking up all of the evidence that there is in support of abiogenesis theory and reviewing it in bitesize chunks for this blog. For those of you who are not well versed in the evidence out there I strongly suggest searching for abiogenesis on the Talk Origins Website, they are much better at explaining it in a user-friendly way than I will ever be (especially since abiogenesis is very far from my field of expertise).

I hope this answers some questions for others as well, and I will always try to answer your questions to the best of my capabilities, so don’t hesitate to voice any concerns (but do hesitate on the trolling, for that I don’t have time).

Sources: Lee et. al (1996) A self-replicating peptide Nature: 328 525-528

Wednesday, May 16, 2012

Thoughts On: Babies and Drunks

This has been a theory that I developed on one of those long college nights, and I thought it was worth sharing. As the combination of alcohol, very little sleep and good company tends to do, my and my roommate's humor threshold was becoming surprisingly low, and thus he came up with the idea of watching youtube videos of people falling down. I have to say that I will never understand why we as human beings find it to viscerally funny, and maybe a theory to that effect will enlighten me on another night. However, on this night my roommate made the keen observation that babies and extremely drunk people fall in a very similar, very distinct way. 

As soon as he said it I understood exactly what he meant. Usually when people fall down we expect some kind of reaction: arms flaying, bracing the fall, even a wince would suffice. When it comes to these two groups of people on the other hand there is none of that, they just seemingly fall in slow motion and just let it happen, and therein lied my theory as to why.

Small babies still need to learn that falling down hurts. The normal reflex reaction to feeling yourself fall is something that is not yet instinctive in babies, because of the fact that they have not felt that pain enough for it to have developed. This is why I think they just fall over, it never occurs to them to brace the fall because they have yet to learn what falling means.

Alcohol, on the other hand, is known to slow the reflexes, and being seriously drunk slows them significantly. Because of this, my theory is that drunk people may know that falling hurts, but they don't realize they're falling until it's too late. By the time their brain has processed the information that it is falling so they should do something about it, they have already smacked the ground.

Of course when I first came up with this in the wee hours of the morning my roommate thought it was genius! By the light of day it seems far less so, although I do not see an evident flaw in my hypothesis. What do you think? Any conflicting ideas to put up for debate?

Monday, May 14, 2012

Tough Questions: Would You Be OK With Your Child In Porn?

Don’t even ask me how this topic happened to pop into my head, it is a (fun? defective?) part of my personality to run with a topic in my head and not let it go until I follow it to its logical conclusion, and is one of the main reasons that I started this blog. It happens when there is an apparent conflict in my head, and as soon as I spot one it needs to be resolved.

The premise is this: I am one of those feminists that believes women should not be demonized because they want to take naked pictures or go into porn. Some women are exhibitionists by nature, they love it and their thoughts and opinions should not be judged differently because of it, any more than you should judge a woman stupid just because she’s blonde or a black man uneducated because of his accent. Yes it is true that there is some very misogynistic, violent and disgusting porn out there done by actresses that are drugged or have serious emotional problems, but that is an entirely different issue and certainly does not represent the entire sex industry. You can fight exploitative porn without thinking that porn itself is harmful or misogynistic in itself, and I am one of those people. When I hear stories of women getting fired because they did porn once or enjoy burlesque dancing
it sickens me.

This position being firmly held in my mind, I realized that the contradiction came up when I realized that if a close family member like my mother or my daughter came to me and told me that they were thinking of doing porn, I would have a problem with it. Well why is that? If I truly believe that there is nothing inherently wrong with doing porn, why would I not want someone I care about to do it? I should support them, not try to convince them not to, unless there is still a part of me that is actually not OK with the sex industry. So, where does the problem lie?

I suppose that it comes from the idea that I would rather my daughter, my best friend or whatever would have more opportunities at her disposal. I would want my daughter to be educated, have a job in which her mind is valued, not her body. I would never want my daughter to have to “resort” to porn, or stripping, because she feels there are no other options. I don’t want my loved ones to be objectified, but most importantly I would not want them to have such low self-esteem that they would want to be considered an object, or less important. I would never want them to feel that they don’t deserve better, or (as would be the case for a daughter) to fall into something they don’t really want to do and have to suffer the consequences of those choices later in life.

However, really thinking about it, I realized that when you think of such a situation you automatically assume that those would be the reasons your daughter/mother/best friend would go into the sex industry, and there I am making a huge mistake which is not fair to many. If my daughter really loved the sex industry, if it is something that inspires her and truly makes her happy, I think I would support her. If she goes into it empowered, proud of herself and with no less self-esteem than she would going into any other job, I would be fine with her choice and defend it to anyone who dares tell her she can’t do it. I’m sure I would never actually be able to watch it, that goes a little too far for me, and of course I will have to have a daughter to put this theory to the test, but I hope to be a better person than to ever deny my child the right to choose her own path in life.

What are your thoughts on the subject, on porn itself? What would you think if you’re family wanted to get into porn?

Sunday, May 13, 2012

Book Review: 11.22.63

I have a confession to make: Stephen King is my guilty pleasure. I discovered him in middle school, and ever since then I haven't been able to go a year without devouring a few of his novels. I know that some of them are flops, and there was a period of time in which he seemed to get a little lazy in his writing, but I've been enjoying his more recent efforts enough to buy a copy of his newest novel: 11.22.63.

I guess one of the reasons I like Stephen King so much is that he writes easy entertaining books, but he writes them well. He has a way of describing certain things, of throwing these sentences into the story with a wording that you've never thought of before, but can never find a more perfect way to phrase that sentiment from then on. It betrays an intellect that I admire (however "low brow" you might find his novels) and lets me become absorbed in his books without being distracted by bad writing (Dan Brown I loved your idea in the Da Vinci Code and it was the only thing that kept me through, but my god take a writing class). Another thing about him is that he always keeps you on your toes. Some authors are dark and brooding, so you know the book will end in horrible tragedy for everyone involved. Others are incredible softies so you know the main character will find a way to pull through in the end. With Stephen King you never know what he'll do. Sometimes he'll kill the guy, other times he'll save them, other times everyone dies but one, other times he tells you someone's gonna get it but you don't know who until the end. It's the fluidity in his style that keeps you glued to the pages, never giving you the security of what to expect.

Stephen King seems to have moved away from the pure horror category he became famous for, and 11.22.63 is another example of this. The premise is this: there are certain moments that redefine the course of history, and one of them was undeniably the assassination of President Kennedy in 1963. If you could go back in time and change it, would you? What would happen, and what would be the consequences?

I don't want to give away the book, but I will say that although I enjoyed it, I didn't enjoy it for the reasons I thought I would. I thought I would be wowed by the creativity of the aftermath, instead the book really takes a different tone than I thought it would. Nevertheless you can see that the research he put into it was remarkable, and he managed to capture the feel of a stranger in a strange time as best as I could expect. I enjoyed Under the Dome more in that it was more suspenseful, but I found 11.22.63 to be a pleasant, definitely more PG Stephen King. I was not up until the early morning glued to the pages, but there's nothing about it that I can say I didn't like.

Friday, May 11, 2012

Yes I'm Happy, Let Me Tell You Why

So by now I'm sure you've all heard about the French elections, Sarkosy (or as I like to call him French Berlusconi) finally got the long overdue kick in the ass that he deserved, and the new Socialist government is in place! It seems as though that Italian fatalism is internationally infectious however, and people seem to be elbowing their way to the front of the line to roll their eyes at the cheering crowds. Do you really think that this guy is going to be any better? He's just slightly more to the left than Sarkosy, but he's still just a politician. Are you really so naive as to think that he will start changing things for the better out of the goodness of his heart? He's not going to take on Germany, ridiculous! I'm not naive and I don't think that rainbows and candy are suddenly going to start raining on the streets of France, but that doesn't mean that I can't be excited about these elections.

I get that it sucks that politics often comes down to voting for the lesser of two evils. Ideally there should always be someone that truly represents you, but usually that is far from the case. However, saying "there is no real progressive here so I'm not going to vote at all" is so, so wrong. What always ends up happening is that the worst of the two (or more) gets elected, and there begins a trend towards disaster. If politicians feel that the public wants a more right wing government they will modify their positions to fit that ideology. Look at what happened in the US for example: the trend has gone so far to the right that if you were to shoot Obama back thirty years (and made him white) he would be perfectly happy in the Republican party, whereas Regan today would be decried by Fox News as a bleeding heart liberal. Every election year we see this trend worsen, and if the people do not speak through the ballot boxes it will only get worse.

I am happy because in France they are finally taking a step in the right direction towards normality. No the new government doesn't have to fix the world, tell Merkel to go fuck herself or keep all of their promises. Like evolution I expect this to be a slow and laborious process, not a quick leap to perfection. However I hope that these elections will change the shift towards a more progressive government, as politicians start modifying their behavior to appeal to what they finally understand is a more progressive people. Even a small step in the right direction is better than none at all, and I think that many need to realize that, stop moaning that they don't live in a Utopian society and do what is in their power to make it better.

So, good on you France. I hope next time around you do even better.

Tuesday, May 8, 2012

Thoughts On: Generalizing

So generalizing has a pretty bad reputation, one that may not be entirely undeserved but one that is getting worse and worse as our society becomes ever more PC. I mean generalizing is just one step up from stereotyping, and from there it's a straight shot to racism! Slippery slope and all that. So it will come as no surprise that, when in a conversation with a friend of mine the other day I happened to make a comment about people in Dublin based on my personal experience after living there for five years, my friend jumped down my throat. You can't generalize! I know loads of people that are not like that! Just because you met people that were like that doesn't mean that they all are! I want to take a moment to defend generalizing, because I'm getting very very sick of having to repeat "yes, I know not everyone is the exact same person".

At this point another little insight into the Italian mentality that I have often described before: I only get verbally smacked if I generalize about other countries or cultures. In the same breath, my friend went on a tirade on how shitty Italians are. They're cheap! They're rude! They never pay you back if they borrow money! They're obsessed with looks! All the girls are anorexic! Why? Because there's this one girl in my gym that is there from morning till night! You know a generous Italian? It must mean that they want favors from you later on. I know Irish people that are generous, that means that they're not cheap at all, at least not as cheap as Italians! You get the idea. Putting this amusing hypocrisy in demonizing generalizing aside, on to my defense.

Life is variable. This is the first lesson of science and statistical analysis and it is just as applicable to people and cultures and customs. Of course if you make a comment like "Irish people are boozers" it does not mean that they all are. It does not mean that they all get hammered every weekend to the point of getting in trouble and/or forgetting where they were and what they did and/or waking up in a strange place with their shoes on the wrong feet. It does not even mean that all Irish people approve of such behavior or would ever allow themselves to get sloppy when they have a drink with friends, if they even drink at all. It is not about thinking that all Irish people are the same, and it certainly is not about meeting an Irish person and automatically assuming that he or she is an unreliable alcoholic - that is where you fall into the trap of stereotyping and down the slippery slope towards racism. However, I submit that it is still in the spirit of discussion of commenting on or comparing cultures that you are allowed to make such a statement, not in the spirit of prejudging someone, but in comparing what is socially acceptable.

I know extremely sloppy drunks that are Irish and I know some that are Italian. I also know people from both countries that don't drink. However, I feel more justified in my previous statement based on what is socially acceptable in either country and what is not. Take these two examples from my life there:

1. I was sitting in a pub with about 10 of my classmates having a beer. A friend walked in and sighed over how desperately she needed a drink. She then went on to say "lads, I haven't had a drink in a week." The table gasped. Why the hell not? Were you sick? Not a single drink?! You poor soul, let me buy you one!

2. I had been up all night writing my thesis and I was exhausted. I was in the common room with a classmate and I mentioned that I was so tired that I could have easily laid down on one of the desks in the common room and fallen asleep. She said "well go ahead, don't worry, if anyone comes in they'll just think you're drunk". I was perplexed. I asked: "are you telling me that it is more socially acceptable to sleep on a desk in a common room because I'm drunk than it is socially acceptable for me to be sleeping there because I was working all night?" Apparently, the answer is yes.

I know that both of those examples come from college and therefore my generalization might only apply to Irish students, but enough drunken nights with my friends' parents tell me that it can extend to the older generation as well. Anyway, my point is that in Italy, getting so drunk that you fall asleep in public in the middle of the day is NOT socially acceptable. In college a friend might laugh about it, but you will be teased incessantly and may people will lose respect for you. If you get sloppy one night you usually spend the next day apologizing profusely to everyone you were with, not proud of how much crap you got up to. Getting hammered with your parents is almost unheard of. It's not that no Italian has ever done any of this, it is that culturally speaking this behavior is outside of the norm, it is the exception, whereas in Ireland getting drunk with your parents is nothing to be surprised about.

And now in typical Italian fashion I have to follow up with a pejorative generalization about Italians, lest I be deemed a naive sucker. One thing that Italians are is jealous. Not necessarily in the boyfriend-girlfriend sense (although there is plenty of that as well), but in the jealous of each other sense. Example: I recently got back from Brazil (which I'm sure you're all sick of hearing about), but I went during a period in which most people don't take a vacation. I also came back with a bit of a tan, it being a tropical country. One day I forgot to moisturize and I was peeling a bit on one arm, and one of my friends said to me "I hope you peel and completely lose all the tan you got over these two weeks!" In other countries that would be considered a terrible thing to say, hateful at worst, rude at best. Here, on the other hand, such a comment is perfectly normal and what I expected her to say, because Italians are jealous people. Sure she was half joking and didn't really mean it, but it would have been inconceivable for me to get offended by such a comment. It is a  culturally acceptable comment to make, which is why I feel justified in saying that "Italians are a jealous people", even though my friend was probably not all that jealous in this case - demonstrated by the fact that she made the comment, it's the ones that say nothing and look at you funny that you want to watch out for.

So that's my two cents on the potential value of generalizing. What do you think? Are you also a generalizer of sorts in the fashion that I described, or do you think that it has absolutely no place in a discussion on cultural differences?

Monday, May 7, 2012

A Little Lesson In: Bahian Fruits

So I mentioned in my post about Salvador that one thing that unbelievable about the region is the amazing fruit that they have, not just in deliciousness but in variety. I could never imagine that there could exist so many different kinds of fruit in one place, and apparently even people that live there their entire lives have not tasted them all. I went on a mission to taste as many as I could, and while I could never get my hands on all of them I do think I made a good dent. I wanted to give you a post on what I learned, and I'll list them in order from worst to best.

Before I offend any Brazilians here's a little disclaimer first: Many of these fruits are generally North East Brazilian fruits and not only found in Bahia, and some of them are found in the rest of Brazil, so this is not to give all the awesome fruit credit to Bahia alone.

15. Jenipapo

This was one of the first fruits I tasted, although by far the one I liked the least. It is a soft brown fruit the size of a very large fist, but soft almost like a foam ball. It is often used in the production of liquor, but you can also either make juice from the internal flesh around the seeds or eat the outer mesoderm the way it is.

It tasted like ass. Raw spongy mushroom ass. I definitely would not recommend it, and from here we move on.

14. Cacau

When I first saw this in the supermarket I thought how interesting, and like an idiot I didn't realize I was holding a cocoa pod, despite the fact I knew what they look like. I just never thought they were sold like that in the supermarket. It turns out, however, that once you manage to cut through the incredibly tough pod, it is very common to make a juice out of the white fleshy bit that covers the cocoa seeds. After that you can sit and painstakingly peel each seed, which initially are purple and taste horrible. Give them a couple of days in the sun however and they turn black and voila! Your very own pure cocoa. 

My assessment: the juice is alright, but it doesn't really taste of much. As for the seeds, if you're the kind of organic chocolate person who likes it nice and dark you'll love throwing a couple of these seeds into your milkshake or ice cream. I, on the other hand like mine nice and milky, so it wasn't really for me.

13. Mamao

Mamao, a.k.a. papaya is one of the few tropical fruits that is (relatively) easy to find in Europe, and yet I had never tasted it before going to Brazil. It is not that I was never interested, but I knew that I don't know how to choose a good one, and that if the mangoes you get over here are any indication it is very easy to get one that sucks. For this reason, having heard such good things about it and not wanting to ruin the experience I waited, and finally in Brazil I had my chance. 

Honestly I was expecting much more. It's not that it tastes bad, it's acutally quite good, it's just that it's not much. My mother would call it a "delicate" flavor. I call it nothing to get excited over, more something that fills you than something that I would ever seek out.

  12. Graviola

This little guy looks like a pear from the outside, but it turns out it's that elusive "guava" that I've heard referenced so many times but never actually seen.

As I've hinted at before, many of these fruits are used to make juices, basically by blending them with some mineral water. As is the case with this one often the juice then has to be filtered as well, as the seeds are quite hard. The juice is OK, also not out of this world but not bad either, but it really goes well when combined with others. They also make a strange dark red jam out of it which is very sweet, and more commonly you'll see a stiff slice-able variety. If you're the sweet jelly flavor type this one is definitely for you.

11. Caju'

This has to be the most interesting looking fruit so far, like a bean squashed into a very small apple. The bean-shaped part actually holds a nut that is very popular in Brazil, almost like the peanut in the US, but the fruit is also commonly eaten and used in juices. It is a little spongy, and by itself I think it tastes a little funky, but it goes very well when you're making a mixed juice, somehow lending its flavor to complement others.

10. Carambola

  This fruit is often used in salads and fish dishes because of the fact that it has a tangy not-too-sweet flavor. However if you allow it to ripen enough it is can be very good to eat alone, the only flavor I could ever come close to comparing it too being a nashi pear (although more in texture than aything else). It's crunchy and it's refreshing, but at the same time not sour, which for me is a big plus.

9. Caja'

Looking at them you'd think they're kumquats, but in taste they're actually the farthest thing from them. They have a very little meat to them and a very tough interior, but the little flesh they do have is bursting with flavor. They are a little on the sour side so I wouldn't eat them just the way they are (unless, unlike me you're one of those sour freaks), but I can attest to the fact that they are wonderful in a caipirinha. Caja', sugar and cachaca makes one awesome cocktail that I definitely recommend.

8. Acerola

 These little fruits are full to bursting with vitamin C, and every bit as sour as they look and then some. I don't think that even a sour fanatic can eat them by themselves as is, although they rank this high on the list because of the amazing flavor they pack in that tiny package. In fact my favorite juice mix that I invented while I was there was caju', graviola and acerola. Graviola for the sweet, caju' to mellow it out, and acerola to pack the flavor punch that strawberries can only dream of.

7. Umbu

This little green fruit, on the other hand, is not as sour as it looks. I only tried it in it's juice form, but it had a very interesting flavor. It just tasted green, if that makes any sense at all. OK, maybe it doesn't, but I can't think of any other way to describe it. I suppose it was closest to the carambola in it's tangy freshness, although I enjoyed more as much as I was intrigued by it.

6. Maracuja

Although passion fruit is another one of those tropical fruits that are found in Europe I had always seen what I later found out to be the African kind: tiny little green/purple balls that lay on the palm of your hand. Imagine my surprise then when I go to open up one of these very large yellow wrinkly things only to find the exact same passion fruit interior. 

Unfortunately not being a sour kind of person it was impossible to eat with a spoon no matter how much sugar I added, but it does make a mean juice when combined with mango as well as a fantastic cocktail.

5. Cupuacu

This is another incredibly strange looking fruit that tastes much, much better than it looks. I only had the opportunity of tasting it in ice cream form, but I definitely was not disappointed. It makes a slightly green ice cream, also quite tangy, with an almost chewy texture that I had never come across in a fruit ice cream before.

4. Mango

OK, so I already knew that mango was one of my favorite fruits, but this trip to Brazil only reconfirmed it for me. The mangoes in Brazil are unlike any mango I have ever tasted, they have many kinds and they really did blow my mind. Always sweet soft and full of amazing flavor, they were a regular feature for breakfast for me.

3. Jaca

This is probably the ugliest fruit when seen hanging from a tree (or worse split open on the side of the road) and it was almost impossible for me to imagine what it must look like inside. However once it is cleaned and packaged you see this huge bumpy woody thing contains these little yellow pods, stiff and juicy, and absolutely fabulous. It is the sweetest fruit I've ever tasted, with a flavor that was completely unexpected and not like anything I can describe. It is a little on the heavy side, and I couldn't really eat to much of it in one sitting, but that's not for lack of trying.

2. & 1. Pinha and Acai

 The next two just have to share a top spot because it would be impossible for me to have to choose between them. This one is a pinha, a strange pine cone-shaped fruit that when frozen and blended makes one of the most delicious things I have ever tasted in my entire life. Granted I was getting it from a place that made it particularly well, blending it with a little condensed milk making it a creamy, heavenly sensation.

The second is this little fruit that may look like a blueberry at first, but the flavor is the farthest thing from it. This is acai, probably one of the most iron-filled foods there is. It is shipped frozen then broken and blended, usually with a banana for creaminess (although not being a fan of banana myself I think it tastes much better with strawberry or cupuacu). It is more refreshing and less heavy than the pinha cream, and has such a particular taste that I still dream about and miss desperately. In two weeks that we were there we only went two days without eating these two, and now we are trying to find a place in Italy that might make it as well. 

I find it to be quite an experience to have so many new things to try in such a short time, and finding so many that are completely new flavors. Imagine someone never having tasted a strawberry before, or a peach, and asking you well what does it taste like? What is it similar too? Well nothing, it tastes like a strawberry! You have to try one and see for yourself. That was what it was like for almost all of these fruits, and it's exciting to me that when I go back there will be just as many more new ones to try. One thing is for sure though, when I go back the first thing I'm eating is another acai, cause I just can't stop thinking about it.