Archive for: October, 2011

What is Skepticism

Oct 31 2011 Published by under Uncategorized

There seems to be a theme running around the intertubes today... a them about skepticism.  I'm nothing if not unoriginal, so here are my thoughts on the matter.

Skepticism is not saying everything is wrong.  Skepticism is saying that you aren't sure of something without further evidence.

Skepticism is not making up arguments to support your thoughts on the subject (pro or con).  Skepticism is honestly trying to find the information that you need to stop being skeptical.

In that way, skepticism should be about data, logic, and the scientific method.  Every scientist should be a skeptic.   But skepticism does not mean doggedly defending your point of you beyond the realm of rationalism either.

Many people claim to be skeptics.  Some of them even are.  Most are not (about something).  We all have our pet notions.  "If I wear my lucky socks on game day, then the Cowboys will win."

Skeptics can be convinced by sufficient information.  That's one way in which evolution-deniers and climate-deniers are not skeptics.  They cannot be swayed by sufficient information.

Muller is a skeptic.  He thought climate scientists were wrong.  He spent two years looking at the data... not to prove the climate scientists wrong, but to find the correct answer to the question he thought was important.  He got the results of his work and is now convinced that the Earth is warming.  I think he remains skeptical about human causation of the warming trend, but maybe he will continue his research.

Watts is not a skeptic.  He is a denialist.  He said he would change his mind and accept whatever Muller found, but he has not.

I could go on and on.

The point is that a skeptic can change his/her mind to fit the evidence.  Does that mean a skeptic must have every possible answer complete?  No.  If every possible question was answered, then scientists would be out of a job.  It would all just be making license plates from then on.

At what point can a skeptic make a decision one way or another, well, that all depends on the question, the evidence, and the skeptic.  As Carl Sagan said, "extraordinary claims require extraordinary evidence".

For Muller, it was 2 years of heavy data analysis.



5 responses so far

Why are Selfish Genes Selfish?

Oct 31 2011 Published by under Uncategorized

Mutations are a fact of life.  Heh, indeed mutations are required for diversity of life.  There really isn't another way to get novel changes to DNA or RNA without it.

I think we can all agree that RNA strands are not alive... in the same way that viruses are not alive.  But they do exhibit some of characteristics of life.

If you will allow me a brief diversion: While I was teaching, a student asked me what the purpose of life is.  Without hesitation, I said, "reproduction".  Of course, the 14-15 year old boys in the class thought that was hilarious and the student seemed quite put out. (I suspect she was attempting to elicit a philosophical point in a science class that she could badger me with.)  All living things die, I explained.  However, when an organism reproduces, it gives some of its genetic material to its offspring.  In that minor way, that organism can influence all future life on the planet.  If an organism dies without passing on its genes, then those genes are lost forever.  There could have been a human 25,000 years ago that was born immune to HIV (not that HIV existed back then, but that's not the point).  If that human didn't reproduce, then its unique ability to be immune to HIV was lost and it will likely never reappear in the world.

This was before I learned that there was an immunity to HIV in the human population.  It's basically the selfish gene concept.

But are genes really selfish?  Obviously, they aren't 'selfish' in the human emotional way.  But, the gene that reproduces the most gets more offspring out in the world and becomes a larger percentage of the total genes in the population.

When I was in high school, I used to say that the human species is breeding for football players and cheerleaders.  Actually what we're breeding for is sex craving men and easy women.  It's true.  I had my first child recently (several years ago), yet most of my high school classmates have multiple children, all much older than mine.  In fact, there are two grandparents from my graduating class.  My genes are being out competed in the human population (which is not really a bad thing considering my genes).

So, its not selfish, it's just better at spamming the environment with copies of itself.

I was going through my abiogenesis papers to find something interesting for you.  I found this. Dr. Joyce does a lot of neat work and although not really an abiogenesis researcher, he has made some interesting discoveries in the field.  This paper describes an experiment in which the experiment was destroyed because of a 'selfish' RNA.

In vitro evolution experiments are very cool.  Basically, you take a RNA (or DNA) and amplify it using a reverse transcriptase and a polymerase that are known not to make perfect copies.  One of my favorite articles using this technique is also by Joyce. The object (as shown in Darwinian Evolution on a Chip) is to evolve a sequence that is better for particular function.

But, something to be careful of is mutations that cause selfish RNAs to appear.  In this case, RNA Z appeared.  This new RNA was successful in competing for resources in the reaction, yet did not perform the desired function at all.

In other words, it is a more successful replicator, but not more successful at doing what it was supposed to be doing.  In this case, it even has evolved some modifications to get around the system that Dr. Joyce used to prevent such a thing from happening.

In this experiment (as I understand it), the desired target product was also necessary for the continued replication of the RNAs.  RNA Z got around that.  I'm sure the paper explains it, but I am not up to that level of biochemistry.  The paper contains a diagram showing how the substrate and promoters and RNAs and DNAs all interact.

After reading this, I am reminded of Jurassic Park (the book, not the horrid movie).  Life finds a way.

Again, this just serves to emphasize our inability to truly separate life from non-life in a meaningful way.  We can't draw the line here anymore than we can draw the line somewhere in a ring species.

8 responses so far

My Project

Oct 29 2011 Published by under Uncategorized

I am hesitant to discuss much of this as I normally don't talk about my work.  There are good reasons for that.

You see... I'm the enemy.  I am a content specialist for a major producer of standardized tests.  My specialty is (duh) science.

Now, I've been in this industry for 3 years now and let me tell you, it's not what you think it is.  Unless you are in the industry or actively involved as a client, you can't imagine what it's like.  I can share a few things with you.

It takes over 18 months for a question to go from an idea in someone's head to an operational item (that means it's scored and the score counts for whatever the test is for).  Each question, depending on the project requirements, will be seen by 2-3 content specialists (usually each one more than twice), artists, copy editors, fact checkers, clients, client committees, and a bias/sensitivity expert before ever even seeing a test form.  Then there is field testing, data review, final review by the client... then it MIGHT get on a test.

The first thing most people think of when they hear 'standardized testing' is the recently ended No Child Left Behind and maybe Obama's Race to the Top programs.  I will say that it is my opinion that these standardized tests in these contexts are used for entirely incorrect purposes and at incorrect times.  But those are client decisions and "him what pays, says".  But there are a lot of tests that have to be standardized that you might not think about.  Every industry that has some kind of certification exam has standardized tests... nurses, IT techs, aircraft mechanics, etc. etc.  Those are generally used properly.

When I say properly, let me explain.  What is the purpose of a test?  To see if the tester knows something.  Now, a well designed test question will not only tell you if the student knows the information, but can also tell you why the student got it wrong.  That last bit is critically important and why much of the high school testing... isn't properly used.  There's accountability with no chance at improvement. If the tester doesn't learn, then there' s very little point in doing it... if you don't learn, there's very little point in doing anything.

A properly designed test should have a diagnostic component.  Which is a pre-test.  What does the tester know now?  It can identify areas of improvement and even (sometimes) over clues into the misconceptions the tester has so they may be taught correctly.  Any assessment is a tool that students, teachers, parents, state officials can use to see what's going on with education at their level.  Unfortunately, it's not being used this way (mainly because it is expensive).  Again, there's a big difference between public school assessments (which are free for the students to take) and professional certification tests that are not free.

But why a standardized test?  Well, that just means that over a given period or group, all the testers take the same test.  Their are several reasons for this.  One is so that scores can be compared between students, schools, classrooms, socioeconomic groups, gender, ethnicity, ect.  And yes, we do compare every test question in every single one of these ways to check for issues.  Because tests are standardized, they can even be compared year to year.  Usually a group of questions are carried over from one year to the next and these form the basis of some extensive statistical analyses to determine how students compare year over year.  It is truly staggering the amount of information that is developed from these tests.

It can go even further.  A few of you may remember Obama's "Sputnick Moment".  Well that's from another standardized test (PISA) that is given to students all over the world.  The same questions given to students in 70+ countries.  The US didn't do so well in the latest one, hence the "Sputnick Moment".

Another complaint that people often have about standardized testing is that it is too easy to guess.  99% of the time, the questions are 4 option multiple choice.  Well, that is changing.  A number of industry leading companies have a variety of new products out.  Items that are hot spots, where a tester selects one or more portions of an image and the computer tabulates the location of each click to determine a score.  Drag and drop, which is a glorified matching question, but often with some advanced features.  There is even some significant research into computer scored essay questions.  I've seen a demo and it is absolutely stunning.  It is not a word count type of system.  It is a learned relational database.  It can tell the difference between a BS answer with lots of technical terms and one that has the exact same terms, but correct.  I've seen it.  It is truly amazing tech.

Sorry for the digression, but I hope that this has given you some insight into the industry.  Like any industry, there is a lot of proprietary technology, processes, clients, etc.  I can't get into that.  If you have any questions, then I'll try to answer them if I can... the more general the better.

But standardized testing is here to stay.

Now, on to my project that I am epically excited out.  This is really a pinnacle of the career type of thing.  I am responsible for the development of the science standards for a MAJOR client.  This isn't state wide or even national.  We are likely to go multi-national with it.  Now, I'm not doing this by myself.  There is the client, various advisory committees, consultants, consultant groups, and a host of businesses all involved.  But I'm the guy that is actually putting the words on paper.  Which means, a lot of what I say will be incorporated into the science standards.  I've made a number of changes and recommendations and the client seems to pleased.

My trip to New York, next week, will be the first of a series of committee reviews of these standards.

When I think about, which I try not to do, I am excited that I am working on such a major project.  Then I get seriously nervous.  What if I say something wrong, what if I didn't push hard enough to get something vitally important in or get something that ends up a waste of time out?

I actually started another draft document today and that's why I'm thinking about this now.  We're talking about being an influence (however small it might be) on literally hundreds of thousands of students a year.

I can say for certain that evolution will be a major theme.  The client unambiguously agrees with me and a consultation group that I assembled from experts in science education.  We're not going to beat around the bush either.  Common descent, speciation, selection, etc.  will all be fair game.  I am very happy about that.  Even if students don't believe it, they still have to learn it and they will learn what evolution is really about instead of the misinformation that is promoted almost everywhere in the US.

I'm just babbling now... and as usual... I'm not sure where to stop.  So, if I can answer any questions you might have, let me know.

13 responses so far

A Brief Survey of Abiogenesis Processes

Oct 28 2011 Published by under Uncategorized

As promised, we'll get away from the philosophical stuff (as much fun as it's been) and on to some of the current state of abiogenesis.  I will borrow some previous articles I've  written on Cassandra's Tears, but I'll try to update them as we go.  My vacation is over and I've learned I'll be traveling to New York middle of next week for work.

What is abiogenesis?

Well, a long time ago, some scientists proved that abiogenesis didn't happen and creationists have been arguing about it ever since. Francisco Redi showed that flies lay eggs on meat, but meat does not generate maggots.  Lazzaro Spallanzani* showed (sort of) that sterile broth doesn't make critters either.  Pasteur made Spallanzani's experiment better and basically proved abiogenesis is impossible.

Oh wait.  No he didn't.  He proved that spontaneous generation of living things from inanimate matter was effectively impossible.  This has absolutely nothing to do with abiogenesis.  A point lost on 47% of US citizens.

Abiogenesis is the formation of living things from non-living matter, but how is that different from spontaneous generation?  Well, Redi and the others were looking at modern organisms appearing without having parents.  Mice born from sacks of grain, that sort of thing.  Abiogenesis is the idea that the first 'living thing' on the planet was produced via chemical reactions.  Once a replicator exists, then it can spam the environment with copies of itself.  Presumably, the organism copied itself imperfectly and the idea of species were born.

I'll say up front that, most likely, we will never know exactly how life on this planet came to be.  Many of the ideas I'll describe here are not incompatible, so it could have been one method or multiple methods, each contributing a piece to the puzzle.  This, of course, is where we get into the determinism vs. contingency discussion again.  We won't, but this is where it would go.  🙂

Given that though, it would be trivial to falsify the concept of abiogenesis.  If any experiment showed that a critical step was chemically impossible, then the concept of abiogensis would be in serious trouble.  However, at this point there are numerous pathways for several major chemical groups, so even if one path were falsified, it is likely we could find an alternate path that would work just as well.

So, what are our options?

The first, and probably the most popular, is the RNA World hypothesis.  In general, this hypothesis suggests that because RNA can be both a carrier of genetic information and act as an enzyme to speed up chemical reactions, that RNA came first.  This hypothesis is supported by the relative ease by which some nucleic acids are made from non-biologic sources.  The famous Miller-Urey experiment didn't form nucleic acids, but then this paper successfully overcomes some of those issues.

Our findings suggest that the prebiotic synthesis of activated pyrimidine
nucleotides should be viewed as predisposed30. This predisposition
would have allowed the synthesis to operate on the early
Earth under geochemical conditions suitable for the assembly

Now, there are some issues with the RNA world.  To date (as far as I'm aware) there has only been one case of a self-reproducing RNA developed.  It is not, shall we say, elegant.  It would be very difficult to form and a pretty exact sequence of nucleotides is needed. Unfortunately, neither of the authors (Tracey Lincoln or Gerald Joyce) see their work continuing along these lines.

The beauty of the RNA world is that it takes care of a lot of the details that we think of when we think of life.  Reproduction, evolution, heredity, and chemical metabolism (kinda) are all there.  These are the pieces of life.  What it lacks is a a couple of critical pieces that are missing are that we haven't built self-replicating RNAs that are simple enough to assemble spontaneously.

Here, I'd like to insert a possibility that is not very popular, but it is relevant.  The idea of panspermia.  Now, this isn't the older "aliens seeded the Earth with life" notion.  But it is known that the conditions in space produce large volumes of organic compounds, including nucleic acids.  So, that's another method that sufficient quantities of organic compounds could appear on Earth.

OK, the next big idea is that of the Iron-Sulfur World.  This concept is significantly different from that of the RNA world in that this is a 'metabolism first' idea rather than information first idea.  Iron sulfide minerals have been found to have some very interesting catalytic properties.  The other major difference is that this would take place in the deep ocean, near undersea volcanic pipes.  Similar to the Miller-Urey experiment, if you put a bunch of volcanic products in really warm water in the presence of iron and nickel sulfides, you end up with some interesting compounds.  Like the methyl thioester of acetic acid and thioacetic acid which are simple analogues of acetyl-CoA.

As far as problems with the Iron-Sulfur world, what it doesn't have is reproduction or heredity.  It does have a powerful metabolism and the ability to synthesize a wide variety of organic compounds.  So, we're missing a key element, genetics.

There are a number of other hypotheses within this area of research.  The clay models, the lipid world, the PAH World, etc.  The important thing to note here is that very few of all these different concepts are mutually exclusive.  Which leads me to my preferred explanation...

All of them.

Why not?  You get the metabolism from iron-sulfur world, the genetics from RNA-world, the long chain molecules from the clay model, and combine them.  Hence my thoughts on the contingency of life.  What if the Earth was too cool to have volcanoes?  Then we would lose a big chunk of the ability to get organic compounds from inorganic sources.  There are a lot more 'ifs', 'ands' and 'buts' here.  But I think this is a good way to go.  Not thinking like a reductionist "this hypothesis is supported" but like a lumper "look at all the hypotheses that are supported".

We have some good ideas for how cells came to be and homochirality too.  More on that later.

I know this is a very brief look at these.  There is A LOT to explore in this area.  I've done some research blogging on a few of the articles I've mentioned here.

If you guys have any questions or concepts you'd like to explore, let me know and I'll try to get some material and put something together for it.


* Spallanzani's name always reminds of me of Dr. Lizardo... 5 internets if you can remember what movie that name is from.

57 responses so far

What Makes a Cell Alive? and a joke

Oct 26 2011 Published by under Uncategorized

OK, last post about this, I kinda promise.  I was thinking about this and reading Luisi's book and he asked another interesting question... one that reflects part of the discussion yesterday.  If you survive all the way to the end, then you will be rewarded with my favorite (and only) Halloween joke... just to show I can do stuff besides ask pointless question.

Let's put aside the question about the difference between an apple and its tree and whether a dead thing has live cells and get to the fundamentals.

Take the nucleus out of an oocyte, as in the cloning experiments, is the nucleus living? And is the cell, without a nucleus, alive?

Now we get even more fundamental. The cell itself. Can it be alive without some parts? If so, which parts? Venter and his colleagues made a cell with scratch assembled DNA.  There have also been various attempts to make a minimum cell by removing pieces until the cell no longer functions.  I don't think this tells us very much about what it takes to be alive though.  Even a minimal cell has all the functions that we normally think of a required for life.

On the other hand, we know that to continue living, a cell must have correct DNA.  Venter's team missed a single nucleotide and the entire organism died.  It must have been a critical function for life.

I think that a lesson we could take from this example is that life has to have instructions.  It there has to be some underlying component that can tell a living thing how to do all the things that it needs to do.  Again, we often think of a living thing as reproducing, metabolizing, responding, moving, and growing and developing.  So the cell has to have the instructions to do all those things.

But leads me to a very unsatisfying definition of life.  "The ability to do all the things that living things have to do."  A better circular argument hasn't been seen, I think.  But, I think we're on a good track.  What is the purpose of life?  If you go with the selfish gene concept, then the purpose of life is to spam the environment with as many copies of yourself as you can.  What do all the copies have in common?  The genes, the genetic information to create copies of itself and the ability to keep itself alive to make those copies.

Could we define life as “the existence of genetic information (enough to operate and reproduce the organism) AND the ability to maintain and/or propagate that information”?

That one sentence, after all of ten seconds reflection, really does a nice job of summing up the functions of life and still allows room for the existence of forms of life other than organic systems (e.g. computer based life or non-organic based life).

Since the horse, as a unit, cannot maintain or propagate the genetic information it contains, it is no longer alive. Same with the apple (which is still problematic to me). For a while, the dead organisms can use internal resources to maintain, but not propagate the genetic information. But it cannot continue the process for longer than the cells have resources.

A bacterium, on the other hand, does have genetic information and can maintain and propagate that information.

The cell without a nucleus is an interesting question, even with this definition. But a little thinking about my definition might reveal a new concept (one that human scientists don’t seem to like dealing with).

Alive may not be an all-or-nothing state. It may even be reversible in some situations. Perhaps the cell, without a nucleus, is dead. But by putting a new nucleus in, then the cell can become alive again.



A vampire bat returned to its cave.  It was covered in blood.

The other bats crowded around it.  "Where'd you get the blood?"  "Look at all the blood."  "Comon, don't hold out, where's the blood from?"

Finally, tired of the incessant whining of the other bats, he said, "Fine.  Follow me."

All other bats followed him out of the cave.  The flew across the field.  They flew over the river.  Finally, they flew into the forest and landed on a tree.

The other bats were so excited.  "Are we there yet?" they cried.

"Almost.  You see that big tree right over there, the really tall one?"

"Oh yes," they all replied.

"I didn't!"

10 responses so far

Why Are Dead Things Dead?

Oct 25 2011 Published by under Uncategorized

Here's another brain twister for the day.  I was kind of hoping for a particular response to yesterday's "Are Apples Alive?" post and I got it this morning (thanks Arthur).

Now, I'm not trying to be difficult I promise, but if an apple that is in the fruit bowl (we'll assume recently picked) is considered to be alive... then why is an animal considered to be dead, when many of its cells are still functioning after we declare it 'dead'?

Our organs can survive for a fairly prolonged time in the event of the whole body death.  Limbs can survive as long as 6 hours.  Bone and ligament, much longer.  Hair and fingernails continue to grow after  death.  The brain can survive for about 10 minutes under optimum conditions without major damage.  There is at least one case of a cat being completely revived after one hour of death.*

Now, I freely admit that we're moving beyond scope a bit.  We're talking about brain death and clinical death here and the prior conversations have been about living things.  But I think that this serves to emphasize a point that I made earlier.  Biology is squishy.  It is very difficult to objectively and completely define some parts of biological systems, because there are always exceptions and, thanks to 3 billion years of evolution, life is very, very tough.  To paraphrase Neil Stevenson, "We come from a long line of stupendous bad-asses... because every living thing in the history of the Earth that wasn't a stupendous bad-ass died quickly."

OK, let's get back to where we were... when considering a multi-celled organism, can we say that it is alive if all of its cells are alive as Arthur suggests?  Yes, of course, the cells in the apple are alive, but is that enough to be considered alive?  If it is, then why is our animal dead, when the majority of its cells are alive and will continue to be so for quite a while?

The direction I'm taking here, is that an apple fallen from the tree is not that different from a limb that has been severed from the body.  That part, whatever it is, can survive for a time, but it is no longer connected to the super-structure that makes the entire thing alive.  A living thing can reproduce itself in its entirety, a broken off portion probably cannot (let's not get into Planaria right now).  A living thing can intake material and energy, which is then used for maintenance, movement, response to the environment.  A broken off part cannot (again, in general, plant cuttings may work fine**).

BTW: In case you are wondering, I'm totally off my planned material at this point and thinking 'outloud'.

Can we say (should we say) that a multicellular organism is no more than it's component parts?  Or is a multicellular organism something like what we were previously talking about... is there something that makes it more than the parts.  Is there an emergent property that says we shouldn't treat single-celled and multi-celled organisms in the way (with respect to being defined as 'alive')?

But research seems to indicate that there is little difference between single-celled organisms and multi-celled organisms at some level of evolution.  This report basically describes the change from single-cell to multi-celled due to predation. (for for the Springerlink link, I thought I had the full article downloaded, but I've lost it).  So, again, life is squishy.  There's not a dividing line between single-cell and multi-celled, so it will be (probably) futile to discuss a difference between life and non-life from that angle (and thus we see an example of real science in which we take a shot and it didn't quite work how we intended).

Or do we go back to the multi-celled structure having specialized cells and all the parts can't function unless they are connected (however tenuously) to the other parts.  The whole organism can do all the functions of life, but pieces cannot.  The cells in my reproductive system, while vitally important to the whole and the species, just can't do their job without the lowly small intestine.

I very well may be obsessing about this too much and am being silly.  I don't think so, but what do I know.  I think this is very important thing to consider.  Not because we'll change the definition of life and biologists will stop studying prions or something silly like that.  I don't want biologists and computer scientists to get into turf wars over who gets to study some digital organisms and not others.

I do think, that at some point, probably in the near future, some scientists will go for it.  They will endeavor to create life in a large, complex simulation.  Maybe it will be a giant Uery-Miller set-up with clary substrates all over and pyrite chunks for catalyzing, put a wave machine in to create vesicles on the clay.  Will it work?  We won't know until someone tries.

But, if we aren't sure what life is, how will we know if they succeeded?

OK, I'll go away now, I'm just blathering.  The plan is to talk a little bit more about this concept of what is live, then get into some abiogensis research and see some of the really cool stuff that is being done to examine the questions of what is life and how did it get here?


* Hossmann KA et al., KA; Sato, K (1970). "Recovery of Neuronal Function after Prolonged Cerebral Ischemia". Science (American Association for the Advancement of Science) 168 (3929): 375–6. doi:10.1126/science.168.3929.375. PMID 4908037.

Hossmann KA et al., KA; Schmidt-Kastner, R; Grosse Ophoff, B (1987). "Recovery of integrative central nervous function after one hour global cerebro-circulatory arrest in normothermic cat". Journal of the Neurological Sciences (Elsevier) 77 (2–3): 305–20.

** Which brings up the whole issue of stem cells.

7 responses so far

Are Apples Alive?

Oct 25 2011 Published by under Uncategorized

Here's where we get to some interesting questions on what is life.

Chapter 2 - Question 3

Is an apple – hanging on a tree – living? When it falls to the ground – is it still living?

This isn't a silly question

Wow, now we get to the meat of it. And this is where I start to have fuzzy thoughts on the subject. It all depends on how you define ‘life’. If reproduction is a requirement for life, then the cell in the apple are probably alive, but the apple itself is not. The seeds are the result of reproduction in the parent tree, not in the apple it self.

This article relates an interesting story about that.

What is the definition of life? I remember a conference of the scientific elite that sought to answer that question. Is an enzyme alive? Is a virus alive? Is a cell alive? After many hours of launching promising balloons that defined life in a sentence, followed by equally conclusive punctures of these balloons, a solution seemed at hand: “The ability to reproduce—that is the essential characteristic of life,” said one statesman of science. Everyone nodded in agreement that the essential of a life was the ability to reproduce, until one small voice was heard. “Then one rabbit is dead. Two rabbits—a male and female—are alive but either one alone is dead.” At that point, we all became convinced that although everyone knows what life is there is no simple definition of life.

To use the classic definition of life that I was taught many, many moons ago. Life has these characters: Composed of cells, has metabolism, grows, adapts, responds to stimuli, reproduces, and maintains homeostasis.

I kind of like that definition, but an apple is not alive by this definition. The cells within it are, but the apple itself does not grow, reproduce, respond (except chemically), or has a metabolism.

Can we separate the living thing from the cells it is composed of? i.e. if the cells reproduce, does the organism? If the cells retain metabolism, does the organism?

I ask because a dead organism may have most of its cells function even after the organism itself dies… at least for a little while.

Which brings us to another question, that maybe we should consider first.

Chapter 2 - question 1

Do you believe in the utility attempting to give a definition of life?

I do think that there is utility in dealing with this question now. Avida organisms can already evolve complex logic functions. And computers are beginning to approach the computing power of the brain (cat brains first) and the human brains processing abilities.  (I will note that there is some skepticism on whether IBM has actually reached the equivalent computing power of a feline.) With that in mind, the question of what is alive will become very important… or maybe not. Humans have an unfortunate tendency to use resources and organisms regardless of the ethical considerations involved.

Life is like porn (you knew I was going there right?).  We might not be able to define it, but we know it when we see it... or do we.  Avida organisms are something that's pretty close to any reasonable definition of life, but they are definitely not made of cells.  Could there be other non-cellular life that we would just ignore because we don't see cells?

So what are the qualities that life must have to be considered life?

Honestly, I've been thinking about this for several months (in those 12 seconds between when I can finally lay down and when I actually go to sleep... otherwise known as 'spare time').  It is extraordinarily difficult to develop a definition of life that does not have some exception.  The apple above for example.  Combinations are even trickier.

I have placed an additional burden in that I think that digital organisms could eventually be alive.

11 responses so far

Determinism, Cotingency, and the Accident of Mankind

Oct 24 2011 Published by under Uncategorized

Well, we seem to be off to a good start.  I do have work tomorrow, so I'll just get this in now and let everyone stew over it all day.  The best sauce and all that...

Since we already kind of got started in this direction, I'll put in questions 2 and 3 from The Emergence of Life - Chapter 1.  This link is to my review of chapter 1.  Here's a link to the book on Amazon (I get no income from this).  But at the least you'll understand the thinking behind determinism and contingency.  [NOTE: You'll find I link to Wikipedia a lot.  It's a convenient location for much of the material that I think you might benefit from.  I do not consider it an authoritative source, but the references and further reading are often  peer-reviewed works that will describe material in detail, with authority.]

Chapter 1 - Question 2:

Do you accept the idea that biological evolution is mostly shaped by contingency? If not, what would you add to this picture?

First we need to talk about contingency and determinism. In the book, Luisi describes determinism (in this context) as the notion that life can develop purely by the interaction of chemical and physical processes. In other words, if the chemicals are available, life will develop. The opposite of this thought is NOT that there was an intelligent designer or something like that.

The other position is that of contingency. That is, the interaction of many factors (the majority of which may be deterministic) is required in an unlikely sequence of events to result in life. Contingency is something like chance, but not quite. Luisi describes it as this way. Contingency is getting hit on the head with a piece of tile roof. The deterministic factors (your walk to work, the poor condition of the roof, wind, gravity, etc) all combined to result in you getting hit with a piece of tile. Another way to look at it is what I call the “re-do” effect. If you reset everything back to the way it was before you walked to work, would you still get hit with the tile? If we reset the universe back 6 billion years and let it run again, would be in exactly the same place we are now?

In my mind contingency is the philosophical equivalent of chaos theory.

Now to answer the actual question. Is biological evolution mostly shaped by contingency?

First, this is a rather curious statement considering the focus of the book. Evolution really doesn’t have that much to do with abiogenesis… or does it. It can be shown that evolution occurs with any system that replicates imperfectly. Is a single RNA strand alive? If not, then we do have evolution on non-life and that evolution may drive replicators toward life. However, is evolution contingent anyway? I think so, if only because of the massive amount of potential influences on an organism. Mutations, environmental effects, what actually determines relative fitness, etc are all contingent things. A particular mutation might be great in an ice age, but if it's not an ice age, then it may be useless.

As far as abiogenesis is concerned, before reading this, I was squarely in the deterministic camp. However, contingency makes a lot of sense. It would explain why we haven’t heard from aliens (of course, there are lots of other reasons for that too).

At this point, I’m thinking that life is probably pretty common in the universe. However, I’m wondering how much life exists beyond slime molds (or alien equivalents)? Is multi-cellularity much more difficult to achieve than we might think? With a sample size of 1, it’s difficult to really examine this, but research seems to indicate that being multi-celled is useful and so may be likely once cellular organisms exist.

Intelligence may be less likely than multi-cellular organisms, but again, a small sample size has resulted in little ability to explore.

I can see the value in both positions.  I think the future research that will be done in space exploration may well give us evidence one way or another.  If the deterministic proposal is correct, then we should see a universe filled with life in all kinds of strange environments (more on this later).  If contingency is more correct, then we should rarely see life and even more rarely see intelligent life.  Which neatly segues into the third question...

Chapter 1 - Question 3:

Are you at peace with the idea that mankind might not have existed; and with the idea that we may be alone in the universe?

65 million years ago, dinosaurs were satisfied. They had existed on this planet for over 160 million years (almost a 1000 times longer than modern humans have existed). Mammals existed for much of that time, but they were rarely much larger than mice.

It took a freak accident to allow the rise of mammals, which has resulted in the development of modern humans. Without an asteroid crashing into and utterly devastating the planet, we would not be here. I have no problem with that.

I’m not so sure about ‘alone’. In the sense that humans may be unique as the only sentient species (i.e. capable of ad hominem arguments and recognizing the fact), I can live with it. I’ve read too much science fiction to be comfortable with the idea… I want to believe. But I can live with the idea that we are unique.  That doesn't imply special privilege or a designer or anthropocentrism in my book.  It just means we are lucky.

But in the sense that there are other living things, I don’t think I can be OK with that. I believe that there is too much energy in the universe (in the physics sense) and the likelihood of complex chemical reactions is too great to say with any confidence that Earth is the only planet with life. Since we find organic compounds in the most unlikely of places (nebula and comets) I think that life is not only possible, but likely to exist elsewhere in the universe, perhaps even elsewhere in the solar system. This life, like the dinosaurs may be satisfied at whatever level it has obtained to this point, but I doubt it. Life changes. Darwin and hundreds of years of observation have shown us that life changes and in ways we cannot imagine (reptiles developing a proto-uterus for example).

Again, this is my belief, but if life exists elsewhere in the universe, then intelligence also exists in the universe.

Your thoughts?

4 responses so far

Who is This Guy and Why is He Here?

Oct 23 2011 Published by under Uncategorized

Hi. I’m very excited to be guest blogging here. This is my first guest blogging spot, so please be gentle.

Cassandra’s Tears is where I normally hang out blogging. I attempt to make some really cool science accessible to the non-scientist. I also talk a bit about technology and the anti-science positions. Rarely, readers are treated to a bit of humor or a past attempts at short stories and poetry.

I have always enjoyed science. When I was three, I could shock anyone older than about 30 by telling them I wanted to be a paleontologist and name dozens of dinosaur genera. Over time (more than I’d care to actually think about), I learned a lot about myself.

I still love science, but I love the knowing. I’m not real big into the actual finding out. Basically, I suck at experiment and observation. I’m also easily distracted. I can’t stand to be fixed onto one subject. I’ve never gotten an advanced degree, because they don’t make advanced degrees in general science. Still, I’ve learned a lot on my own and am pretty comfortable with most areas of science.

This stood me in good stead while I was teaching. I taught, for a few years, at a tiny little school in Sabine Pass, Texas. You might remember it being run over by hurricanes Rita and Ike. I joined Sabine Pass School right after Rita and stayed until right after Ike. I taught; biology, chemistry, physics, IPC (physical science), oceanography, and TAKS prep courses… all in the same year. Suffice to say that I know a little about a lot.

I’m a huge fan of science fiction, even though there is little out there worth reading or watching nowadays.

Now, I’m still involved with both education and science. I’m a science content specialist for a company that works in publishing, education, and assessment. So, I get to read all the cool stuff and then try to incorporate that into our products. Yes, I live in a cube farm.

On Cassandra’s Tears, I’m engaged in a chapter review of The Emergence of Life by Pier Luigi Luisi. Abiogenesis is a fascinating topic and so much has been learned in just the last decade. What’s interesting about the book is that the author has included some chapter ending questions for the reader. These aren’t like ‘test’ questions, they are thinking questions.

Those are what I would like to talk about here. I think this would be a good place for discussion. I’m planning on taking a few of the questions about life and the generation thereof and giving you my thoughts about the matter. I would love to hear your thoughts on the matter as well.

“What is life?” and “Where did life come from?” are not simple subjects. I think it’s the nature of biology (being squishy rather than firmly defined).

If you think about chemistry, you can firmly declare a molecule to be of a given type. It isn’t water unless it’s 1 oxygen and 2 hydrogens in a covalently bound system. You can even talk about solutions with varying ratios of solute to water, but you can define them in very specific ways and have a standardized convention for stating how much solute, how much solvent, and the concentration of the solution. So, even if there’s a range, you still have a very specific definition.

You can't really do that for life and there are a lot of 'ifs', 'ands' and/or 'buts' involved.

So, that's what we'll discuss here. Totally new, totally fresh, so let's get the ball rolling. What do you think a good definition of life is?

7 responses so far

So long and stay in touch!

Oct 23 2011 Published by under Uncategorized

Wow, time flies. This is my last day here at Scientopia and it's been a terrific two weeks. Thank you all!

So now you have an idea of what I usually blog about: a few random musings and discussions over research papers, usually the ones I come across as I sail the wondrous world of genetics. And, just because I'm a failed-painter-converted-to-photography, I post a lot of my photos too. Shamelessly, I should add.

The other thing I do over at my blog, but I haven't posted here because I didn't know if it was "in theme," is author interviews. I stalk invite over published authors who are either scientists or whose work (whether fiction or non-fiction) touches on science. It can be anything, from blogging to science fiction, and so far I've got some terrific guests! So, if you consider yourself a writer scientist or a science writer and would like to be my next featured guest, drop me a line -- I'd love to hear from you.

Again, many thanks to the Scientopia community for hosting me, and to all the readers for the engaging discussions. Please stay in touch!

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