UDreamOfJanie

Dream a Little Dream of Me.

What is Science?

Immediately following our oh-so-lovely shower, Kate suggested that I perhaps start at the beginning.


Chapter One, Page One

What is Science? As I currently understand it, science is about figuring out. About explaining.

We see something, we naturally want to know what it is, where it came from, where it’s going, and how it affects us in its passing. Science is about answering these questions.

My darling Kate has been quite adamant about the idea that science is not about knowing, per se. It’s more about understanding better. She’s been educating me on the difference between a theory (as used by the general public), a Theory (as used by science), and a fact.

theory – guess

Theory – expanation of something observed, back up by facts, subject to change as more accurate facts appear or are discovered

fact – 2+2=4. 2+2=4 is true today, it was true yesterday, and it will be true ten thousand years from now

For an example:

Observation – There is a Snuffleupagus in our driveway.

fact – All previously observed Snuffleupagi have been either in or from Snuffleupagusland.

theory – The Snuffleupagus came from Snuffleupagusland.

hypothesis – The Snuffleupagus in our driveway appears to be similar to all other previously observed Snuffleupagi, and therefore may have come from Snuffleupagusland. Further observation and/or testing is necessary to confirm or refute this.

Testing phase – where we attempt to confirm or refute our hypothesis. We could start by asking the Snuffleupagus where he’s from. His answer is that indeed, he flew on a C-141 Starlifter straight from Snuffleupagusland International Airport to Albert J. Ellis airport in Jacksonville, NC.

Theory – As all previously observed Snuffleupagi have been either in or from Snuffleupagusland, the Snuffleupagus himself gives us compelling support for our hypothesis, and no current information contradicts our hypothesis, we can say for the moment that the Snuffleupagus probably originated in Snuffleupagusland, but future observations may cause us to alter or abandon this theory.

Sometime later, we travel to Albert J. Ellis airport for a flight to Cancun, Mexico for some nude sunbathing. When we enter the airport and talk to Isabel, the lady behind the counter (who is very sexy, and has great hair), she chuckles. “Take a look out the window at that inky dinky runway. We only fly to Charlotte NC and back in little teeny tiny planes. We have one small jet that makes a shuttle run to Philadelphia International once a week, but that’s all we can handle with our inky dinky runway.”

Thinking back to the Snuffleupagus, we of course ask the question…

“What about the C-141 back and forth to Snuffleupagusland?”

In a fit of uproarious laughter, Isabel shows us a picture of a C-141 Starlifter. “First of all,” says she, “a C-141 Starlifter is a military jet. It would have no business at a civilian airport. Second of all, look how big that sucker is. Our runway isn’t even wide enough for something like that to taxi, let alone long enough for it to execute a takeoff or landing.”

Our next hypothesis and investigation may involve Snuffleupagi and honesty, but for now, let’s go back and re-visit our original theory.

We now have reason to suspect a problem with our “Theory on the Origins of the Snuffleupagus in Our Driveway”. We won’t throw it out just yet, but we need to go back and investigate the discrepancy.

Did Isabel lie? Did Mr. Snuffleupagus? Did we perhaps misunderstand Mr. Snuffleupagus’ testimony? Is Mr. Snuffleupagus really a Snuffleupagus? Could he be an abnormally large anteater impersonating a Snuffleupagus? Perhaps Mr. Snuffleupagus is a different, rare species of Snuffleupagus, the heretofore only rumored Small Penis Forked Tongue Snuffleupagus, snuffleupagus javisonadus.

We need to go back and do more research. After Cancun, of course. And a private drink or two at Isabel’s apartment.

How am I doing so far?

Filed under: Biology, Education, Humor, Science

63 Responses

  1. Lifewish says:

    Pretty damn good, actually.

    This is a matter of personal opinion, but I tend to emphasise the predictive aspects of science over its explanatory aspects. Science is a crystal ball, the ultimate tarot set – it tells us what we’re going to see next. In some ways, science itself is an evolutionary process – we generate lots of new crystal balls (hypotheses) and then ditch the ones that produce borked predictions. Over time, we home in on the clearest crystal.

    I like this version because it also gives us a reason to want to study science and make sure our answers are right, above and beyond our natural curiosity. If we study science, if we work all the imperfections out of our crystal ball, we can figure out which of our actions will produce the best results. Will digging in a particular spot uncover a transitional fossil? Will applying genetic algorithms result in more efficient engines?

    Incidentally, as a maths grad I am legally obliged to point out that 2+2=4 is a theorem not a fact – it’s an inevitable consequence of a particular set of fundamental mathematical axioms.

  2. JanieBelle says:

    lifewish said
    “I tend to emphasise the predictive aspects of science”

    Ahh yes. Kate and I hadn’t gotten to the “where it’s going” part of the post yet, but she was just explaining that this is the real power of science. Great Minds Think Alike, it would seem.

    “Incidentally, as a maths grad I am legally obliged to point out that 2+2=4 is a theorem not a fact – it’s an inevitable consequence of a particular set of fundamental mathematical axioms.”

    Okee Doke, lifewish. One thing at a damned time.

    🙂

    I’ll try and think of something to edit into my “fact” portion of the post that’s a little more accurate. Kate actually just pointed out that “All previously observed Snuffleupagi have been either in or from Snuffleupagusland.” is also subject to change, so I’ll figure out something to adjust that to, as well.

    Kisses to lifewish for your help.

    JanieBelle

  3. DaveScot says:

    Good, JanieBelle.

    If you would, look up “methodological materialism” and “philosophical materialism”, distinguish between the two, and describe what role if any each plays in the scientific method.

    Next please define “evolution” and “intelligent design” in a paragraph each. Much misunderstanding occurs because evolution and ID can mean different things to different people even in the same context.

    If “evolution” is defined as descent with modification from one or a few common ancestors and ID is defined as the best explanation for the occurence of some patterns found in nature is intelligent agency then we can stop right there as there is no conflict with “evolution” and “intelligent design”. The problem usually comes in when philosophical materialists insist there is no significant possibility of intelligent agency (other than human of course) that does or ever has interfered with the natural course of events in the causally connected universe. Methodological materialists (that’s me) say that in principle intelligent agency in the universe can be investigated by the scientific method. SETI is an example of such a research program. The other major problem is that ID supporters in large number believe the God of Abraham is the intelligent agency and harbor no open mindedness to any other agency or lack of any agency at all. Neither the God-belief nor the philosophical materialist belief belong in scientific endeavours. Science is agnostic and it goes where the evidence leads.

    That bears repeating: Science is agnostic and goes where the evidence leads!

    If the evidence leads to life as we know it being best explained as an accident then so be it. If the evidence leads to life as we know it being best explained as the work of intelligent agency then so be it. I happen to believe the evidence, at least in the case of chemical evolution (abiogenesis), is lacking. Spontaneous generation, which in essence is what the philosophical materialists are forced to accept as an axiom because of their philosophy, is a worn out concept that should have died back in the dark ages when it was believed that mice spontaneously generate in grain storage bins. But because of philsophical materialism being strong where it doesn’t belong (in science) we are asked to have faith that spontaneous generation is a fact and we just don’t know the details yet. The only fact is we don’t have any details. The possibility exists that there ARE NO DETAILS because spontaneous generation NEVER HAPPENED.

  4. JanieBelle says:

    Ok, Dave. Thanks for that.

    That being said, just to avoid getting mired down again in the ID/evo war, how about if for the time being, we work with what came after the “one or a few common ancestors”.

    That way, I can work on science without spill over from the culture wars.

    Everybody OK with that I hope?

  5. blipey says:

    Okay. Unbelievable. I’m going to try to address this without mentioning __________. That will be hard, of course, but I think, doable. Any thoughts that I might be referencing information introduced by ______________ is purely coincidental. If anyone has question about my post, I will be happy to not answer them, unless they are from jb or ck.

    Science is agnostic and goes where the evidence leads!

    Yes, which gets us back to the Science Thread topic of “where’s the positive evidence of design”?

    Is this it?

    The only fact is we don’t have any details. The possibility exists that there ARE NO DETAILS because spontaneous generation NEVER HAPPENED.

    Not a lot of positivity there. Or this:

    I happen to believe the evidence, at least in the case of chemical evolution (abiogenesis), is lacking.

    Well and good. This is still negative. Where is the evidence FOR design?

    intelligent agency in the universe can be investigated by the scientific method.

    How? I’m not saying it can’t be, but how? And, perhaps more importantly, what kind of intelligence?

    The ID comparison of itself with archeology is ludicrous. We already know humans were the cause of the things we’re looking at and for. We make all of our inferences based on the fact that we KNOW the general intent and MO of the intelligence. IDiots say we can know nothing of the designer, so our only source of info in the matter immediately dries up. How are the two “disciplines” alike at all?

    The comparison to SETI is equally flabbergasting. SETI is looking for signals that stand out. It makes no inference as to why they stand out. It makes no conclusion as to intelligence. In fact, if something weird were to be found by all those radio telescopes, the first (and probably next 39) thing SETI researchers would do is try to find a natural explanation for said findings. They would not say, “Oh, there must be intelligent creatures making this signal.”

    ID has provided no basis to reliably infer design from non-design unless all introductory conditions are already known. Since ID expressly states that these conditions are unknowable, it cancels itself out.

  6. JanieBelle says:

    Ok, blipey, thanks for that.

    But what about my original post here?

    Is there anything you’d like to see me tweak or understand better about the basic ideas of science before we even go any further.

  7. blipey says:

    I will echo Lifewish. The power of science is its ability to tell us what questions we should ask.

    Dave said something similar, too, when he said science goes where the evidence leads. But, it goes further than that: it tells us where we might start looking for the next answer.

    If a particular theory poses no questions or provides no new areas to explore, it is useless–a science stopper.

    Your Snuffleupagus story was great, it provided you with a constant line of new questions. Evaluate the scientific merits of other, non-Snuffleupagusarian, theories similarly.

    How to Spell Snuffleupagus -jb

  8. JanieBelle says:

    Crap, I forgot that the recent comments script doesn’t like smilies in the first line. Now I have to hit MYSELF with the Big Green Marker…–jb

    😛

  9. Lifewish says:

    I’d just mention that there are in fact two definitions of “materialism” or “naturalism”. The first (which I think is the one that Dave is using) says “thou shalt not arbitrarily invoke ghouls, goblins, Gods, or other paranormal entities”. The second says “thou shalt not invoke explanations which cannot be tested for accuracy”.

    The first definition is a handy rule of thumb – people have a bad habit of blaming things on paranormal critters, and this “rule” just reminds us that in most cases that’s a mistake. The second definition is generally held to be pretty much fundamental to science. For more on testability, the philosopher Karl Popper is a good place to start.

    The reason I’m mentioning this is that this sort of thing causes a lot of confusion, with people arguing over whether divine intervention would count as a materialistic effect or not (in the first sense, it wouldn’t; in the second sense, it would). Plus, testability is a cool concept to play with.

    Dave: can you confirm whether this post is vaguely accurate? I’m no philosopher and I don’t want to be mangling your definitions.

    Kate: tell Dave and I to quit it if we’re messing up your syllabus for Janie’s philosophy-of-science education 🙂

  10. JanieBelle says:

    Kate is taking a nap (I guess I just wore her tough but cute Marine butt out.)

    😛
    I’m going to follow her lead here, so I’ll be back in a little bit. (I guess she wore my cute Civilian butt out, too.)

    😛
    I’ll work on the predictive power of science as it relates to our example then.

    Kisses,
    JanieBelle

  11. JanieBelle says:

    Ok, we’re back. After our nap and the incident in the mudhole.

    I’m pretty beat though, so if it’s all the same to you fellas, we’ll take this up in the morning.

    Kisses,
    JanieBelle

  12. Anonymous says:

    Also, we look for repeatability in science, as part of its predictive nature. For example, if your mother went out after you and asked the same snuflupagus where it came from and it answered that it came from somewhere other than snufllupagus land, then that is a data point against your hypothesis. Or at the very least it suggests that your chosen method of measurement, ie talking to it, is inadequate methodologically speaking, as in, it leads to differing answers.

    hmmm, I might be trying to push the metaphor too far.
    guthrie

  13. JanieBelle says:

    No, we get the picture just fine, guthrie. I don’t think you’re stretching the metaphor at all. I think I’m following you just fine.

    Kate and I have been going over the predictive power of science.

    She was just talking this morning about how that one cloning guy came out with a paper (talking about how he cloned a person or something?), but no other scientists could repeat his experiments and get the same result.

    That’s why the papers in science journals have to be so specific and full of technical terms, right? (Of course that makes them terribly difficult for me to read.) So that some other scientist, on the other side of the world, can do the exact same experiment and get the exact same result.

    Tangent – Doesn’t this sort of rule out Medicine as science, though? For example, if Dr. Joe gives me a particular medicine for a particular ailment, and Dr. Fred gives Kate the same medicine for the same ailment, we might have different side effects. Also the medicine might help me, but not Kate.

    I certainly don’t mean any disrespect at all, but wouldn’t that make a Doctor more of an artist than a scientist?

    Good to see you ’round guthrie. We’ve missed you lately.

    Kisses,
    JanieBelle

  14. Lifewish says:

    Tangent – Doesn’t this sort of rule out Medicine as science, though? For example, if Dr. Joe gives me a particular medicine for a particular ailment, and Dr. Fred gives Kate the same medicine for the same ailment, we might have different side effects. Also the medicine might help me, but not Kate.

    The prediction doesn’t have to be completely deterministic; it’s valid to predict that one of a range of options will happen.

    Say you have a possible cancer cure. The hypothesis is: this drug significantly improves people’s chance of surviving cancer. One possible prediction is: at least 80% of cancer sufferers who take this drug will be alive at the end of five years.

    Of course, the prediction still has to be one that you wouldn’t expect to be true if the hypothesis were false. In practice, doctors figure out whether this is the case by using placebos to make sure that people aren’t just recovering anyway.

    There’s also a whole array of funky statistical tricks to check whether the drug’s apparent effect is sufficiently big to suggest that the drug actually works. I really don’t understand those, though.

  15. DaveScot says:

    JanieBelle

    what came after one or a few common ancestors

    Descent with modification of course. If I hadn’t been following orders I’d have banned every swinging dick on Uncommon Descent that spouted any nonsense about 2+ billion years of descent with modification from one or a few common ancestors not being true beyond a reasonable doubt. The indisputable testimony of the fossil record tells us that much. What it can’t tell us is how the modifications were caused. There’s only so much that imprints in rocks can tell us. For instance, a fossil could reveal a bone that was broken and mended during the creature’s lifetime but it couldn’t tell us what caused the bone to be broken. Similarly, while the fossil record gives us a roughly dated, partial record of the diversification of life, it can’t tell us what caused the modifications to occur.

    So the only real question is what caused the modifications: chance or design?

    That said, I object to throwing out abiogenesis. That is the hardest thing about evolution to explain. If that can be explained as an accident of nature I’m willing to concede that everything that followed was also an accident of nature. If biogenesis was no accident then it’s likely that what followed was no accident either.

    Asking to skip over biogenesis in evolution is dodging the most important question.

  16. DaveScot says:

    Also, we look for repeatability in science

    Yes, indeed we do and past evolution is not repeatable while future evolution is unpredictable and current evolution is undemonstrable. Whoever decided that the study of an unrepeatable, unpredictable, unobserved process should be called a “science” needs his head examined.

  17. JanieBelle says:

    Hi Dave!

    “Asking to skip over biogenesis in evolution is dodging the most important question.”

    I agree in principle here. But I think I need to get a better handle on the easier stuff before I tackle the tough stuff.

    It’s kind of like I’m trying to understand how to operate a bicycle, before I try to understand how well a particular bicycle was designed and built.

    So you don’t buy into the whole “fish with scales, birds with wings, Snuffleupagi with big butts” thing, right? You’re issue with evolution is whether it occurred by happenstance or direction, not whether it happened at all, if I’m reading you right. I don’t want to put words in your mouth here.

    And I DO NOT want to have anyone start flaming Dave.

    If anyone feels they must continue the shooting war on my blog, DO IT HERE!

  18. JanieBelle says:

    And I DO NOT want to have anyone start flaming Dave.

    To be clear…

    His thoughts on science are open for everyone to discuss, CIVILLY. His character is NOT.

    I hope that is understood perfectly.

    JanieBelle

  19. JanieBelle says:

    Dave, your last comment posted while I was working on my following comment.

    I want to look at each of the points you raise one at a time, if that’s ok.

    “past evolution is not repeatable”

    But is it not repeatable because we don’t have the technology or the lifespan to do it, or because it’s impossible? Does it matter?

    If we could, in principle, take a page out of sci-fi and evolve a fully formed adult human (with great hair, of course! If you’re gonna do it, do it RIGHT!) from non-living chemicals , would that necessarily rule out the possibility of Design?

    Would we then have “become as gods”?

  20. DaveScot says:

    JanieBelle

    If you haven’t a priori ruled out intelligent design then abiogenesis IS the easy stuff. It’s easy to explain from a design standpoint. It’s only difficult for the philsophical materialists to explain. DNA and ribosomes compose a program driven robotic protein assembler. In principle no different from the robots that build computer motherboards and automobiles – just smaller and more complex. Computer programming literate members of your generation should have no problem grasping it. You should also have the knoweledge that computer motherboards and automobiles wouldn’t exist without intelligent agency. Complex machinery has never been observed to self-assemble but has been observed to be the result of intelligent agency. Extending this observation to a machine of unknown origin is a reasonable thing to do and don’t ever let anyone tell you otherwise. The UNreasonable thing is to presume it happened by accident without a single shred of evidence that such an accident is physically possible.

    Once one admits that design is a reasonable explanation for the machinery of life then one must also admit that the original design may have been of arbitrary complexity. Designers aren’t constrained by gradualism or starting simple and working towards the complex. Therefore one can consider the possibility that the first life to appear on this planet had a genome DESIGNED to diversify along a predetermined path. And that, my dear girl, explains everything from the fossil record to space exploration in an entirely consistent manner.

  21. DaveScot says:

    If there’s one goal that all life seems to have it’s to reproduce itself. It will use any resources available to accomplish that task and its progeny is more often than not able to move into new locations if needed. Consider a dandelion whose seeds float on the four winds in order to find newer, more fertile ground to continue the species.

    Given that perspective lets apply it to life on earth as a whole. We know that someday the earth will be inhospitable to life. If something else doesn’t get it first our sun will eventually turn into a red giant and incerate the earth. If planetary life follows the pattern of individuals then there must be a mechanism whereby life on this planet can explore its surroundings looking for a new places to start growing – just like the dandelion. What would that require? Well, I’m a bit biased but I’d say it requires a species that can build telescopes to find promising new worlds around younger stars and able to build spacecraft capable of transporting life from here to there.

    Humanity very well may be the final cog, the reproductive organ if you will, in the diversification of life on a much larger scale than single planets. This is why I said in the previous comment that if the original life on this planet was designed to unfold the way it did it explains everything from the fossil record to space exploration. Literally and consistently.

  22. DaveScot says:

    Just for the record, the reason I want to avoid the evo/id controversy is that it is more or less an endless controversy with no winners and lots of verbiage. I have carpal tunnel syndrome in both hands and excessive typing causes it to flare up. So if I say “it pains me to say this” it’s not necessarily just a turn of phrase for me.

  23. JanieBelle says:

    Dave, thanks again for taking the time to discuss this with me. I’m sure you have better things to do, so I really appreciate your efforts.

    Rest assured, I have not “a priori ruled out” design or anything else. I simply don’t have enough information to make that decision. I’ve been trying to correct that.

    OK, I HAVE ruled out bedtime stories from the various “holy books”. It seems patently obvious to me that all that silliness needs to go the way of the T-Rex. Most of it isn’t even good literature. (The Song of Solomon is an exception to that, in my opinion.)

    Computer programming literate members of your generation should have no problem grasping it.

    While I certainly can cut and paste some javascript, and I have a pretty good handle on html, I wouldn’t classify myself as “computer programming literate”. I get your point, though.

    computer motherboards and automobiles wouldn’t exist without intelligent agency

    I see what you’re saying here. I would only point out that the DEGREE of intelligence of the agency seems to vary greatly between brands. A large portion of both automobiles and computers are just crap.

    🙂

    Crap, I see you’ve commented twice more whilst I whittled away here with this comment. I’m ahurryin’!

    The UNreasonable thing is to presume it happened by accident without a single shred of evidence that such an accident is physically possible.

    If we all got together and threw a bunch of chemicals in a pot and let it simmer for a few million years, and when we opened it up we found some bacteria growing (assuming they weren’t already there or artificially introduced) would that constitute evidence for “accident” or do you think that would still be intelligent agency? After all, we threw the stuff in the pot in the first place. Or is it a close enough approximation of early earth to count as “accident”? I’m just thinking out loud, here. I suppose it’s more of a philosophical question than a scientific one.

    Ok, I’m going to post this one, and get to work on your other two…

    Kisses,
    JanieBelle

  24. DaveScot says:

    Evolution is unrepeatable according to Darwinists. Processes whose causes are random are not repeatable in their results. It’s not because we don’t have the technology, it’s because the odds of it randomly happening the same way twice are more than just astronomcally large. On the other hand, if life was designed, it should indeed be repeatable and in principle we could design an organism that would more or less follow any course of diversification we programmed it to follow.

    However, being the open minded fellow that I am, I’m always willing to evaluate any claimed observation of random mutation plus natural selection creating a novel cell type, tissue type, organ, or body plan. So far there has been no such observation and the usual reason given is that the process is too slow to observe making those kinds of changes. How convenient. We have a postulated process that is not repeatable, not predictable, and not observable. That’s science? Not in my opinion. It’s science fiction masquerading as science fact.

  25. JanieBelle says:

    Damn, for a guy with carpal tunnel, you’re just going to town.

    Give me a sec, don’t go away. I actually want to ask something about your most recent comment.

    Kisses

  26. JanieBelle says:

    …it’s because the odds of it randomly happening the same way twice are more than just astronomcally large.

    Ok, with today’s technology, we’re just starting to discover planets around other stars, which is just way cool in and of itself.

    Let’s say that next week or next year, we find us a planet very similar to earth, and not too far away. Let’s further postulate that within that same time frame, somebody figures out how to do the warp drive thing, and we can actually go there by the time the discovery of the planet is made.

    Now, being the curious little devils we are, of course we’re going to send the U.S.S. Enterprise NCC-1701D on over for a visit.

    When the crew arrives, Captain Jean-Luc Picard (Kate likes bald guys) and Commander William “hottie with a beard” Riker, with a full compliment of red shirts just in case, hop out and go poking their noses around.

    What if they find a race of Trans-gender Purple Octopus Aliens. What would that mean for Design?

    What if they found perfectly normal, English speaking humans with great hair?

    What if their journey was interrupted by the Crystaline Entity?

    I know these are silly examples, but I think they’ll work to help elucidate here.

    Kisses,
    JanieBelle

  27. Alan Fox says:

    This link might interest you. The resultant calculation would be dramatically altered by evidence of life having existed or still existing on another planet (Mars possibly the likeliest candidate). Life (that had arisen independently) on Mars would indicate abiogenesis was a common event and we should find extra-terrestrials all over the universe. No life in our solar system could mean (according to the Drake equation) the possibility of life arising is so unlikely that we are on our own.

  28. JanieBelle says:

    That’s funny. Kate had just pointed me there a little bit ago.

    It’s an interesting equation. But it seems like it doesn’t do us much good yet. We may have a handle on R*, but aren’t we still way unsure about fp and doesn’t our lack of confidence increase exponentially the further to the right of that equation we move?

    It almost seems as though we won’t be able to fill in the blanks of the equation until after we already know the answer.

    JanieBelle

  29. Anonymous says:

    I woudl just like to comment on this bit by Dave:

    “On the other hand, if life was designed, it should indeed be repeatable and in principle we could design an organism that would more or less follow any course of diversification we programmed it to follow.”

    So why arent Dembski et al doing that just now?

    As for this:
    “It’s not because we don’t have the technology, it’s because the odds of it randomly happening the same way twice are more than just astronomcally large.”

    I suggest that Janie goes and reads up on mutations in anything that she can find has been investigated.
    guthrie

  30. Alan Fox says:

    It almost seems as though we won’t be able to fill in the blanks of the equation until after we already know the answer.

    You may well be right there. Dembski’s explanatory filter also fits your statement very well. 🙂

  31. Anonymous says:

    Also, by Daves definition of repeatibility, cosmology certainly wouldn’t be science, since we can’t run the universe all over again.

    What matters is repeatable observations leading to predictions which then pan out. In terms of evolution, these focus around the relative structures that organisms have, and the simple fact tha torganisms adapt to environmental changes.
    guthrie

  32. Alan Fox says:

    In terms of evolution, these focus around the relative structures that organisms have, and the simple fact tha torganisms adapt to environmental changes.

    That would be Lamarckism. Adaptation occurs as “beneficial” mutations are fixed in a population by natural selection.

  33. Wonderpants says:

    That said, I object to throwing out abiogenesis. That is the hardest thing about evolution to explain.

    //sigh

    Abiogenesis is NOT evolution. One deals with how life began on earth, the other on what life did after it began.

    The Miller-Urey experiment from the 1950s demonstrated that amino acids, the basic building blocks of life, could form under conditions similar to those of the early Earth. And the acids could have also arrived via comets or meteorites. See
    http://en.wikipedia.org/wiki/Miller-Urey_experiment
    for more info.

    The indisputable testimony of the fossil record tells us that much.

    And evolution doesn’t rely solely on the fossil record.

    What it can’t tell us is how the modifications were caused.

    Aren’t we lucky we already know then: Random mutation and natural selection.

    past evolution is not repeatable

    Under the right circumstances and with enough time, it certainly is. Given enough time and the right circumstances, you could breed chihuahuas back into wolves or even Great Danes, and vice versa, of course (it’s estimated that dogs diverged from wolves around 15k years ago, a mere moment in geological terms). The key is time.

    while future evolution is unpredictable

    Unknown but not unpredictable. The icecaps are melting due to global warming. Therefore I predict that polar bears and penguins will either evolve to deal with warmer conditions or die out because they failed to evolve to suit warmer conditions. Come back in a few thousand years to see if I was right.

    current evolution is undemonstrable.

    – Experiments with fruit flies in labs – breeding them to have 4 wings, red eyes, whatever.
    – Superbugs in hospitals that have become immine to normal antibiotics.
    – The recent alarm over the possibility that bird flu might become able to spread via air from human to human, rather than from bird to bird, or from bird to humans in regular close contact with birds.
    – Bacteria in super clean NASA labs
    – Trout in certain areas of North America
    (Though I can’t actually find information on these last two, so I’ll consider them unsupportable for now).
    All these are examples of organisms evolving very very rapidly indeed.
    So what if it’s ‘artificial’ evolution? If it can happen in one place, it can happen in another.

    Whoever decided that the study of an unrepeatable, unpredictable, unobserved process

    Also known as Intelligent Design

    should be called a “science” needs his head examined.

    Are you volunteering?

    If you haven’t a priori ruled out intelligent design then abiogenesis IS the easy stuff. It’s easy to explain from a design standpoint. It’s only difficult for the philsophical materialists to explain.

    Not difficult to plausibly explain at all, I already discussed at the start of my post.

    I should add here that intelligent design is not ruled out a priori. It’s ruled out because it really is untestable, unrepeatable, and unpredictable (or rather can predict everything – Godddidit – and thus predicts nothing), and don’t be fooled by DaveScot claiming that evolution is exactly the same.
    ID is no different to the ‘watchmaker’ idea that was put forwards by Paley 200 years ago, and which became obsolete as the idea of evolution gained credibility. (PS: Darwin didn’t actually establish evolution singlehandedly. The idea had been floating around for a while before he published Origin of Species, and he only established the method by which evolution occurred).
    And despite 200 years having passed, ID still hasn’t advanced beyond Paley’s day. There’s no genuine evidence for it, it’s backers don’t do any research or publish anything, and, by some interesting coincidence, the immense majority of it’s supporters happen to be fundamentalist Christians, with the occasional fundamentalist Muslim or Jew thrown in for a bit of variety.

    DNA and ribosomes compose a program driven robotic protein assembler. In principle no different from the robots that build computer motherboards and automobiles – just smaller and more complex.

    Except that the robots that build cars and motherboards, or the cars and motherboards themselves, don’t reproduce.

    You should also have the knoweledge that computer motherboards and automobiles wouldn’t exist without intelligent agency.

    Complex machinery has never been observed to self-assemble but has been observed to be the result of intelligent agency. Extending this observation to a machine of unknown origin is a reasonable thing to do and don’t ever let anyone tell you otherwise.

    Can I tell you otherwise?
    You can see humans designing cars and motherboards any day of the week. So where can I see a designer designing cells, bacteria, or whatever?
    Until I can see said cells or bacteria being designed, it most certainly is open to question.

    The UNreasonable thing is to presume it happened by accident without a single shred of evidence that such an accident is physically possible.

    Yet again, see the start of my post.

    Given that perspective lets apply it to life on earth as a whole. We know that someday the earth will be inhospitable to life. If something else doesn’t get it first our sun will eventually turn into a red giant and incerate the earth. If planetary life follows the pattern of individuals then there must be a mechanism whereby life on this planet can explore its surroundings looking for a new places to start growing – just like the dandelion. What would that require? Well, I’m a bit biased but I’d say it requires a species that can build telescopes to find promising new worlds around younger stars and able to build spacecraft capable of transporting life from here to there.

    It may not need a complex, technologically advanced species at all (in fact, it can be very plausibily argued that humanity, or any other large brained/self aware species, may be an evolutionary misstep, given the damage we’re doing to the planet). Bacteria have been observed to survive long term gross extremes of heat and cold, and even zero oxygen atmosphere environments like outer space. As such, they’re more likely to survive near catastrophic events and spread to other planets.

    And if life was designed with the intention that it would spread to other planets, why would those planets be so annoyingly far away, their environments so annoyingly inhospitable, and our means of getting there so annoyingly slow?

    Even the earth is far from ideal for us. If it was designed for us, or we desaigned for it, then why aren’t we aquatic to take advantage of the 9/10s of the earth that is ocean, and why is so much of the land we do have inhospitable (deserts or icecaps)?

    That’s why the papers in science journals have to be so specific and full of technical terms, right? (Of course that makes them terribly difficult for me to read.) So that some other scientist, on the other side of the world, can do the exact same experiment and get the exact same result.

    Yes, I’d imagine that scientific papers are hard to read because they’re not aimed at the man in the street, and because their audiences need very precise information in order to test and replicate their ideas or discoveries.

    But if you choose books by Richard Dawkins, say, you’re going to find them a lot more accessible and easy to understand, as they are aimed specifically at the man in the street. I’ve just been rereading Dawkins’ Climbing Mount Improbable, which I can thoroughly recommend (and explains a lot of evolutionary subjects very clearly and convincingly).

  34. Wonderpants says:

    Damn, I accidentally italicised parts of my comments along with DS’s comments. Can you edit comments?

    I can, and I did. Double check that I got it right. I’ll get to the actual substance in a little bit. Y’all caught me in the middle of fiddling with the site, Kate’s new profile to be specific. – jb

  35. Alan Fox says:

    I’ve just been rereading Dawkins’ Climbing Mount Improbable, which I can thoroughly recommend (and explains a lot of evolutionary subjects very clearly and convincingly).

    The Ancestor’s Tale (also by Dawkins) is also excellent. It can be used for reference, as though it has a linking narrative, the sections can be read as stand-alone pieces.

  36. JanieBelle says:

    Give me a few secs, fellas. I’m trying to add Kate’s new profile to the sidebar. I’ll take care of the edits in just a sec, wonderpants.

  37. Anonymous says:

    Sorry alan, I should have said something more along the lines of what you did. Damn me being a layman at htis.
    guthrie

  38. Alan Fox says:

    No worries, Guthrie. It was a nitpick. Blame Dawkins for teaching me most of what I know about evolutionary biology. As I already posted, “The Ancestor’s Tale” can be a handy source of reference when blogging.

  39. Damn me being a layman at this.

    You’re doing at least as well as I am, guthrie. Don’t sweat it. She’s learning, and that’s what’s important.

    Kisses,
    Kate

  40. JanieBelle says:

    Way back up yonder there, Alan said “You may well be right there. Dembski’s explanatory filter also fits your statement very well.”

    Well as I’m sure the entire world is aware, I’m no scientist…

    However, I’ve seen some reviews of that filter. It doesn’t seem to cover all the bases, to me. Or, it seems to cover too many bases, I guess, depending on how you look at it.

    I’m not a big WD fan these days anyways, in the event that there’s some person living in the jungle who wasn’t aware.

    I understand that the character doesn’t determine the quality of the science, but one DOES have to bear in mind the source.

    guthrie then said:
    What matters is repeatable observations leading to predictions which then pan out.

    I’m glad you brought that up, guthrie. I hadn’t quite gotten my finger on it, but there was something about repeatability that was knocking around in the back of my head and it was bothering me.

    Rather distracting for a blonde to have a thought, you know.

    🙂

    So repeatability of observation must necessarily stand in for repeatability of experiment result in some cases.

    How do we decide when? Where do we draw the line and say “Here you can substitute observation, here you cannot.”

    Or is predictive power the end all and be all of science? Seems like it should be. If it doesn’t make any accurate predictions, what good is it?

    That’s just my first thought off the cuff.

    guthrie continued:
    “In terms of evolution, these focus around the relative structures that organisms have, and the simple fact that organisms adapt to environmental changes.”

    To which Alan responded:

    “That would be Lamarckism. Adaptation occurs as “beneficial” mutations are fixed in a population by natural selection.”

    OK, you guys are dumping huge amounts of information on me, and I’m overloading. What’s Lamarckism? Give me the cliff notes.

    I’ll get to Wonderbritches in a separate comment while y’all work on that.

    Kisses,
    JanieBelle

  41. Lifewish says:

    OK, just got back in for the evening, so I’m working through the posts. Just wanted to address this:

    If you haven’t a priori ruled out intelligent design then abiogenesis IS the easy stuff. It’s easy to explain from a design standpoint.

    I’d rather say that it’s easy to explain away from a design standpoint. Saying that a designer was responsible is a wonderful way of handwaving the issue away but, unless you go into a lot more detail on the designer’s identity and how exactly it went about designing stuff, it tells us precisely jack.

    Allow me to elaborate. A good design hypothesis for, say, the origin of humans might look something like: “the human race was genetically engineered by aliens from Mars, and when we visit Mars we’ll find remnants of the technology they used to do it”. It provides enough detail that each component step (the existence of the aliens, the advancedness of their biotech, etc) can be tested for feasibility.

    A bad design hypothesis might look something like “humans couldn’t have evolved because my maths* says so. Your fossils that would appear to prove the converse are therefore obviously wrong. I’m not going to point out exactly what’s wrong about them – that’s not my job”. This gives any scientist with an interest in the issue absolutely nothing to go on. It’s worse than wrong; it’s useless.

    Back to the original subject. Currently, the only origin-of-life hypotheses I’m aware of that even attempt to drill down to a useful level of detail are the abiogenetic ones. No-one has yet produced a scientifically useful OOL design hypothesis. In fact, there’s a fairly strong feeling on our side of the fence that the ID folks are actually doing their utmost to avoid providing detail.

    If anyone in the ID community can come up with a detailed description of the creation of life that explains, rather than merely explaining away, critical elements of biology, they can count me as their first convert. Until then, I’ll stick with the group that gives the impression they’re actually trying to uncover useful OOL information.

    * I speak as a recent maths grad here. If mathematical results contradict real-world evidence, the majority of the time it’s the maths that’s at fault.

  42. JanieBelle says:

    Wonderbritches said:

    “Abiogenesis is NOT evolution. One deals with how life began on earth, the other on what life did after it began.”

    I thought the same thing.

    Regardless, I’d like to deal more generally with science first, if everyone is cool with that. I’m starting all over here. I have to understand what does and does not constitute good science before I can even look at evolution, ID, abiogenawhatsits, cosmology, Drake, Fermi, Dyson, Von Neumann, Bracewell, Darwin, or Roscoe P. Coaltrain.

    Holy crap you wrote a lot. I really do appreciate all the time and effort you all are putting into this.

    So Miller and Urey took some basic compounds, swished them around in a kitchen pot for a week, and came out with some amino acids and proteins. But what about a living organism? Can we, or have we, done the same basic thing and come out with bacteria or something? What about something else?

    I’m having difficulty articulating this. Life. Alive. Can we come up with something from such an experiment that’s alive?

    Which brings up the next question… What constitutes life? At what point is a pot full of chemicals just a pot full of chemicals, and at what point is a pot full of chemicals alive?

    I’m just musing here, but it seems like you can say “yes, this person is alive” and you can say “no, that rock is not alive”. What about all the stuff in the middle? Ok, we can trim down one end and say “this algae is alive”. We can trim down the other end and say “this bowl of amino acids is not alive”.

    But when you start getting closer to the middle, it seems a little more slippery to me. Ok, we can say that bacteria are alive. A bacterium is a cell, it’s got a certain structure. It replicates. But what about a virus? It replicates and even mutates. But aren’t they a little weird in their structure? Are they perhaps just “less alive” than a tree or a dog?

    I guess I want to ask if there is a definite line where we can say “this side of the line, alive, that side, not.”

    Or are we talking more of a continuum? More relative. Like this has more life than that?

    Ok, break time. My brain is going to explode if I try to bite off too much more.

    Kisses,
    JanieBelle

  43. JanieBelle says:

    Going back to the “what is alive” question for a sec,

    The point of all that was,

    If we DID swish around a bunch of chemicals and came up with something alive, would we recognize it?

    Just because we know what life looks like as it is, does that necessary mean that life couldn’t be life any other way?

    What if our chemicals were different? What if we came up with something totally different than has ever been seen in the history of earth? How do we say “oh, yes that’s alive” or “oh, no that’s just a weird thing we made”?

    Kisses,
    JanieBelle

  44. JanieBelle says:

    Hi Lifewish.

    It’s going to take a bit for me to work my way all the way down to your latest comment. I’ve been remiss in my studies. Everyone popped in while I was off goofing around.

    I guess the general point you were making is about the usefulness of a theory of the Origins Of Life, though, right?

    Kisses,
    JanieBelle

  45. Lifewish says:

    I guess I want to ask if there is a definite line where we can say “this side of the line, alive, that side, not.”

    There’s no strict line. And any time anyone formulates a rule it turns out that there are exceptions. That’s the case with a lot of biology.

    In general, we say that something is alive if it can reproduce and respond in some way to its environment. However, that leaves us with tricky edge cases like: are red blood cells alive? They certainly don’t reproduce. Are viruses alive? They reproduce and respond, and yet most people don’t think of them as being any more alive than a computer virus.

    For that matter, are computer viruses alive? How complex would one have to be before we’d give it that status? Is a simulation of a living cell or organism itself alive?

    At this point, someone usually mentions the Matrix, and the discussion goes downhill from there. With some questions, all you can do is drink tequila til they go away :-/

    I guess the general point you were making is about the usefulness of a theory of the Origins Of Life, though, right?

    Yup. I was basically saying that abiogenesis is probably the oldest field of science to be this incomplete, but at least abiogenesis researchers are following an approach that can in principle lead them to an accurate answer. They’re doing actual science.

    The rest of my post was mostly an unnecessarily snide jab at people who “infer” design, don’t bother to figure out any actual details, and are surprised when people aren’t terribly satisfied with that answer.

  46. DaveScot says:

    wow – much activity

    af – discovery of life elsewhere would be phenominal even if just microbes – I’ve been following SETI and the space program since their birth – hard to believe one time the whole nation was engaged and talking about it then we beat the Russians to the moon and it all wound down – SETI is a program seeking to confirm the Copernican principle of mediocrity which is the principle that launched the age of enlightenment – briefly stated it says that there’s nothing special about the earth – it’s a mediocre planet orbiting a mediocre star in a non-descript galaxy that isn’t the center of anything (ie no special creation). Furthermore, life should be a common thing in the universe not a special creation either. It appears so far that the Copernical Principle has fallen flat on its face this time. The earth may indeed be a very special place. On the other hand, a good explanation for “where are they all” is that the length of time that a civilization is in the radio phase is very short and precedes what has been termed a technological singularity where technological evolution replaces organic evolution and life is catapulted in a cosmic eyeblink to a higher plane of existence that no longer uses radio technology and has no more desire to communicate with life like us than we have in trying to communicate with bread mold.

    As far as books talking about technological singularities, possibly the most influential book and important book I’ve ever read is Engines of Creation by K.Eric Drexler. It’s available in its entirely online. I read it the year after it was printed – 1987. One of the amazing things in it was it predicted the world wide web, hypertext, and now it has been published in hypertext on the www.

    guthrie – paraphrased “Why aren’t Dembski et al designing artificial life?” Because any serious attempt I would think needs billions in funding. The Discovery Institute has an annual budget of a few million bucks. That’s chickenfeed. Get real.

    guthrie – also says cosmology wouldn’t be science by the standard I employed for evolution – BZZZZZZZZZZZZZZT Wrong – because of the finite speed of light we can actually observe the universe evolving by focusing our instruments at greater and greater distances away – and cosmology is predictable – everything behaves according to precise laws of physics. So with cosmology, we can’t repeat but we can observe it happening in the past and we can predict what will happen in the future. Evolution on the other hand is unrepeatable, unobservable, and unpredictable.

    wonderpants – I see you want to dodge the biggest question in evolution – how did the first cell evolve – I don’t blame you for wanting to dodge it but it’s central to the question of design. Sigh all you want if that helps you justify the dodge. You don’t get to define for intelligent design the boundary conditions of what is relevant. For design the most glaring example of it is DNA and ribosomes. Every living thing has them and they are central to the mechanism of descent with modification.

    jb – re Captain Kirk finding life on other planets – this brings up a good point – suppose Kirk was stranded on a lifeless, earthlike planet. He would die but many of the microbes we all carry in and upon us wouldn’t. The bacteria under his fingernails might seed the planet and eventually evolve into something resembling earthlife. After all, the microbes would already have all the needed machinery to replicate and evolve. It would all be DNA-ribosome based life too since that is what it would have started from. If he found English-speaking natives then I presume we could conclude that some english-speaking human civilization is going about colonizing the galaxy and the earth is one of those, whether we knew it or not.

    lifewish – “it tells us precisely jack”. Sometimes the evidence leads to a blind alley. Them’s the breaks. Should we discount the big bang and all the evidence for it because it leads us to a gravitational singularity that we cannot see beyond? Of course not. Science goes where the evidence lead not where we wish it to lead.

    By the way, for all you folks wanting to separate OOL and evolution your disingenuousness is revealed the moment I suggest that life started out with a complex genome and unfolded without any need to generate additional complexity as all the needed complexity was already there in the last common ancestor. You see, Darwinian evolutionists are committed to a certain kind of abiogenesis whereby genomes proceed from simpler to more complex. They can’t commit to this and at the same time refuse to claim it as part of the theory. If they claim it is a separate issue then they shouldn’t object to beginning the evolutionary story with a complex genome instead of a simple one. So it’s really nothing more than an attempt to dodge the most difficult question in the evolution. How life began is central to the question of how it radiated from that beginning. But nooooooooo… the Darwinian apologists want to invent bounds on what the first life was like and then refuse to discuss it from there because they know it’s a invention out of whole cloth but is central to the story that follows.

  47. DaveScot says:

    trivia

    Red blood cells are the only cells in your body that have no DNA in them. They are stripped of their nucleus to make them small enough to get where they need to go. Interestingly, of all vertebrates only mammals have anucleate RBCs except for one genus of salamander.

    However, it’s untrue that RBCs don’t reproduce. They are born with a nucleus and reproduce when young, before they reach the anucleate adult form. What, does someone think RBCs are manufactured as opposed to coming from a mother cell?

    Never ever forget omne vivo ex ovum (everything comes from an egg). Life comes from life in every case ever observed. Every daughter cell has a mother cell. Every cell alive today theoretically has an unbroken cell line back to the last universal common ancestor (LUCA). Then, according to Darwinist’s, a miracle happened, and somehow a daughter cell was produced without a mother cell. Yeah right. In any other science a rule like “life comes from life” with no exception in billions of observations would be a law, not a theory. But not in Darwin-land pseudo-science. The normal rujles of evidence don’t apply for them. If they think something happened a certain way then for them it’s the same as demonstrating it happened that way.

  48. Anonymous says:

    With regards to Alans nit pick, it was my second sentence:
    and the simple fact tha torganisms adapt to environmental changes.
    You could start with this wikipedia entry:

    http://en.wikipedia.org/wiki/Lamarkism

    Basically, Lamarkism would be if your skin turned blue due to an act of will, or accidental ingestion of something, and then your children also had blue skin.
    The famous example was Lysenko in 1930’s Russia, who wanted to plant orange trees going northwards, with the idea that they would habituate themselves to the local climate, then he would plant some of their descendants further north.
    guthrie

  49. Lifewish says:

    By the way, for all you folks wanting to separate OOL and evolution your disingenuousness is revealed the moment I suggest that life started out with a complex genome and unfolded without any need to generate additional complexity as all the needed complexity was already there in the last common ancestor.

    Is this the “frontloading” idea, whereby every gene we’ll ever need is already in the genome to start with? There’s two problems with that.

    Firstly, genes that don’t have any current use tend to degrade fairly quickly. Because they’re not under any selective pressure to stay as they are, they accumulate mutations and stop working. The broken vitamin C gene in humans, as well as being a strong evolutionary prediction, is also an example of this phenomenon. There are many other pseudogenes that testify to the destructive effects of uselessness.

    Secondly, the idea that all the needed complexity was there from the start has strong counterexamples. For example, the Nylon bug is a bacterial strain that recently evolved the ability to eat nylon. We’ve managed to pinpoint the cause down to a single frame-shift mutation in a known existing gene.

    A frame shift is quite a radical mutation, so this isn’t a case of just modifying an existing enzyme slightly. It’s a completely different enzyme, that just happened to have this ability. When you have 10^30 bacteria on the planet, that sort of thing’s going to happen occasionally. It’s dramatic, but not particularly unexpected.

    If they claim it is a separate issue then they shouldn’t object to beginning the evolutionary story with a complex genome instead of a simple one.

    As someone who accepts evolution, I have no problems with starting off with any sort of genome whatsoever and then letting additional cool stuff happen to it. As someone who tentatively accepts abiogenesis, I’ll happily debate that point too. I imagine that this is a fairly standard viewpoint – many of us also like to discuss religion and politics, but that doesn’t mean they’re essential components of evolutionary theory.

    However, it’s untrue that RBCs don’t reproduce.

    Thanks for picking me up on that, I’d forgotten that it was an adult condition.

    Then, according to Darwinist’s, a miracle happened, and somehow a daughter cell was produced without a mother cell.

    What happened was that our model for what constitutes an organism broke down. The same thing happens when you look at the start of multicellular life – a colony of existing organisms became so interdependent that it started to make sense to define it as an organism in its own right.

    The apparent sharp dividing line when the first cell arose isn’t a result of some mystic interaction; it’s a result of our having to switch from considering the RNA chains as the organisms to considering the community as the organism. It’s an artefact of our sloppy use of language.

  50. Anonymous says:

    Ahhh, Daves so much fun.

    because of the finite speed of light we can actually observe the universe evolving by focusing our instruments at greater and greater distances away

    But dave, how do we know that it is evolving? How do we know that it didnt just pop into existence a few thousand years ago?

    And, more importantly, what experiments can we do to test the big bang? Or the evolution of stars?

    Oh, we cant, at least not directly. But we can make observations. Many of them.
    So how is this different from evolutionary biology, where we make observations, make predictions, and keep track of things.


    and cosmology is predictable – everything behaves according to precise laws of physics.

    Indeed- how is this any different from biology, dave? What laws of physics are being broken in evolution, dave?

    Evolution on the other hand is unrepeatable, unobservable, and unpredictable.
    So you say, but you never manage more than an argument from ignorance, or perhaps an argument from restricted personal definition of stuff that you dont want to know about.

    guthrie

  51. DaveScot says:

    lifewish

    Of course I have already addressed the first problem you point out since it so obvious.

    Faithful reproduction of unexpressed genetic material is a trivial design problem. Algorithms used in computer science guarantee data integrity to whatever level is required. There are far, far more complex things found in living cells than mere error detection. Error detection is trivial in terms of resources required compared to error correction. Checksums are not computationally intensive to generate, store, or employ and will, depending on the system requirements, give you as much confidence of data integrity as required. Correcting an error is resource intensive. This requires the storage of a significant fraction of the original data, a greater fraction being required for greater confidence in all errors being correctable. In the instance of preserving unexpressed genomic data in a front loading scenario error detection would be the only thing I’d expect and correction would simply be a matter of destroying the copy containing the error. Since there are presumably many other intact copies the destruction of one containing an error is a reasonable way to assure that all existing copies are error free.

    In your second objection I fail to see how adaptability in a modern bacteria says anything at all about the complexity of a ancient front loaded genome. There may very well be nothing left of that original genome in any extant organism as the diversification plan could, for good reason, be designed to shed parts of the uber genome that would not be used in any descendants of that line. Some means of adaptability to changing environments does not preclude front loading either. A nylon eating bacteria is still a bacteria. It’s already known that Lamarckism is alive and well in the prokaryote world. Recent Scripps research has identified a mechanism where e.coli under stress radically increases the mutation rate of certain genes in a shotgun attempt to solve a problem. Nylonase may simply be a result of that stress response. Bacteria then share their successes with other bacteria through horizontal gene transfer (plasmid exchange I believe is the primary mechanism). I would also point out that adaptation of digestive enzymes isn’t exactly on the scale of novel cell types, tissue types, organs, or body plans. Such level of modification through descent are a requirement of common descent and must be explained in a plausible mannter. The accumulation of changes such as a novel digestive enzyme doesn’t add up to novel cell types, tissue types, organs, and body plans.

    guthrie

    We don’t know that that universe didn’t just pop into existence a few thousand years ago. We don’t know it really exists at all. We may be living in The Matrix. I don’t intend to waste space addressing such questions. You’re a troll making assinine points and this is my last response to you.

  52. DaveScot says:

    lifewish

    What are the odds that a random frame shift will result in a useful enzyme? It’s hard to conceive of a mutation to a coding gene that could be more radical as the frame shift changes every codon down the line from it. Presumably it even creates a new stop codon somewhere.

    Did anyone happen to consider that frame shifting may be a way to efficiently store information and that the nylonase gene (perhaps once used in the past to digest something similar to nylon)? Who knows how many useful enzymes may be generated from frame shifted coding genes. It’s only recently become known that transcription editing increases the number of protein products in the human genome threefold. In a bacterial genome where size is much more important (genome size appears to be directly correlated with cell size and reproduction speed) to the organism’s survival strategy we might expect to find some very clever techniques employed to maximize storage space.

    This brings up another issue I’ve had with some mainstream thought on genome size and information content. As a design engineer I’m absolutely amazed that a construct as complex as a human being could be specified in a gigabyte of storage space (the approximate size of a 3 gigabase genome). To think that ANY of it could be wasted space (true junk) only compounds the mystery of how so much information can be packed in so little space. There’s something we’re missing and it’s big. There are either additional information storage mechanisms like transcription editing in DNA we’re clueless about (I’ve wondered in the past about DNA folding and information contained in the 3D structure of the folds) or, equally likely IMO, is a vast amount of epigenetic information storage in the structure of the cell surrounding the DNA molecule. Considering omne vivo ex ovum there’s no reason to preclude vast storage capacity in cell structure that’s heritable.

    Since we don’t know what those additional storage mechanisms are we can’t really address how they mutate or how they resist mutation. Maybe some or all of the front-loaded information exists outside the DNA molecule or is encoded in the DNA molecule in a manner we’re not aware of.

  53. Lifewish says:

    Janie&Kate: Dave and I are getting horribly off-topic here. Please do rein us in as and when it starts to get irritating or confusing.

    What are the odds that a random frame shift will result in a useful enzyme?

    Fairly low. Fortunately, there are ridiculous numbers of bacteria continually dividing and mutating, so over time a fairly decent-sized portion of the sample space can be explored.

    I doubt anyone has seriously considered the possibility that the frame-shifted information could have been in some way predefined. There are three good reasons for this:

    1) As far as we can tell, frame shifts mutations occur randomly. The chances of a frame shift occurring in just the right place to reconstitute pre-existing code are pretty minimal. We’re aware of no mechanism that could be targeting these frameshifts in any way.

    2) If you have one frame-shifted gene hiding beneath another gene, any silent mutation to the concealing gene will destroy the hidden gene. Silent mutations do not affect the protein produced, so there’d be no immediate problem for the organism – but, when it “decided” to reconstitute the hidden gene, it’d find that it was broken.

    3) If the gene was actually written into the original code, you’d expect it to be far more efficient than it is. The nylonase produced by the nylon bacterium isn’t actually terribly efficient – the reason it’s doing so well is that there’s nothing else fighting for the niche. Of course, it’ll probably get more efficient as time goes by – should be interesting to watch.

    As a design engineer I’m absolutely amazed that a construct as complex as a human being could be specified in a gigabyte of storage space (the approximate size of a 3 gigabase genome).

    We already know that evolutionary processes can actually be far more efficient designers than us mere humans. See, for example, the work of Adrian Thompson, who uses genetic algorithms to evolve new computer circuits (using FPGAs, for the geeks amongst us). From the linked article:

    “Thompson’s work is not aimless tinkering. His brand of evolution managed to construct a working circuit with fewer than one-tenth of the components that a human designer would have used.”

    This is actually fairly standard. Evolution is very good at efficiency, because it has no problems with using the sort of dirty hacks that would make real designers vomit. Dirty hacks are actually kinda built into the methodology.

  54. Anonymous says:

    I suggest its not just dirty hacks. The reason so much “information” can be stored on so little space is that not only does it read back and interact with itself, its that the coding in the DNA produces so many more structures, with their own interactions. Start with DNA. Then proteins, organelles, cells, organs, organisms. So many levels, and as far as we can see, they all interact according to the physical laws of the universe. Thus life is a result of the structure of the universe.
    guthrie

  55. Zachriel says:

    The Scientific Method: hypothesis, prediction, observation, validation, repeat. The scientific method is a recursive system of matching theory with observation.

    A scientific hypothesis is a tentatively held conjecture for the purposes of developing predictions of empirical observations. The hypothesis is just one step in the scientific method. It must then be confirmed through observation. The more successful the hypothesis is at predicting various observations, the more confident we are in its validity. But all scientific findings are considered tentative and subject to revision upon new information.

    (Please click the link to read the entire discussion of The Scientific Method.)

    DaveScot: “Yes, indeed we do and past evolution is not repeatable while future evolution is unpredictable and current evolution is undemonstrable. Whoever decided that the study of an unrepeatable, unpredictable, unobserved process should be called a ‘science’ needs his head examined.

    This is a typical misrepresentation of the scientific method. For instance, let me make a scientific claim — that dinosaurs once roamed the Earth. Well, no one ever saw a dinosaur roam. But we do have their fossilized remains. They have what appear to be legs, heads, teeth, and so on. They resemble other vertebrates in a lot of particulars. In fact, we can reasonably conclude that they not only roamed, but ingested, digested, defecated, copulated. So, even though we cannot duplicate the observation of a dinosaur roaming, roam they did.

    DaveScot: “Evolution is unrepeatable according to Darwinists. Processes whose causes are random are not repeatable in their results.

    We can’t repeat dice rolls, but we can predict their distribution. And evolution as the change in allele frequencies in populations over time can be directly observed, as well as mechanisms of this change such as natural selection, sexual selection, mutation, and genetic drift.

    The defining characteristic of science is the ability to make valid predictions. This might mean predicting the distribution of fossils in the geological strata. Or it might be a prediction of how populations change in response to the environment.

    DaveScot: “You see, Darwinian evolutionists are committed to a certain kind of abiogenesis whereby genomes proceed from simpler to more complex.

    Scientists are dedicated to the evidence. The evidence indicates that all life evolved from primitive replicators, but there are still many unknowns.

    Abiogenesis is not a component of the Theory of Evolution, or Germ Theory for that matter. The first life form on Earth may have been a lucky accident, a natural property of carbon and liquid water, a unique circumstance, seeded by comets, or even a Divine Miracle. The Theory of Evolution concerns the diversification of life, not its origin. However, it is known that life did not always exist on Earth, but that once it began, it diversified into a variety of forms.

  56. Anonymous says:

    Hey, I’m sure i put a post up rejoicing in being called a troll by Dave scot. WHy hasnt it appeared?

    (Those of you who have met me before might know that i am as far away from being a troll as you can get, although I will try and be funny sometimes.)
    guthrie

  57. JanieBelle says:

    I’m not sure what’s up with that guthrie. I’ve lost a few comments myself this morning.

    I’m looking into it.

  58. Zachriel says:

    DaveScot: “Then, according to Darwinist’s, a miracle happened, and somehow a daughter cell was produced without a mother cell. Yeah right. In any other science a rule like “life comes from life” with no exception in billions of observations would be a law, not a theory.

    Um, I’m not sure what you’re saying, but the fundamental unity of life is an obvious principle of evolutionary theory. Not only do dogs come from dogs and cats from cats, but dogs and cats came from a common ancester.

    Nor would a claim to Intelligent Design resolve the conundrum. You would still have a broken continuum of life. Either the Intelligent Designer made life out of the clay, or Prometheus smote the head of Zeus, and Athena, fully armed, came out of the top of the Great God’s head at the river Triton.

    You also misstate the nature of scientific law. Certainly, a consistent observation can be considered a “law”, but even “laws” do not necessarily have universal application. For instance, Boyle’s Law relating volume and pressure in gases only applies to ideal gases in the macroscopic realm. Newton’s Laws of Motion are similarly limited in their domain of applicability.

    With regards to abiogenesis, there is a schism between chemistry and biology, just as there is between Quantum physics and the physics of Relativity.

    Theories of Quantum physics and Relativity do not cease to be valid scientific theories because they are yet to be reconciled. They operate largely in separate realms, though Inflation Theory offers a glimpse into plausible unification. Similarly, there are no processes in organisms that cannot be traced to electro-chemistry, but the unification of chemistry and biology is not still not yet known.

  59. Anonymous says:

    Ah well, its not hugely important. Either way, I shall continue to address points raised by Dave.
    guthrie

  60. Alan Fox says:

    I’m sorry I can’t spend more time here, as debating an opposing view, forces one to verify and refine one’s own position, a great way to learn new stuff. Which is why I found UD and its suppression of any sceptical comments so frustrating.

    I read through the thread again and see many of Dave’s points answered. (I have to say, Dave, if you can rein in that petulance so well (as, for the most part, you have here) that surfaced so frequently elsewhere, I would petition an unbanning at PT and AtBC.)

    However one remark:

    As a design engineer I’m absolutely amazed that a construct as complex as a human being could be specified in a gigabyte of storage space (the approximate size of a 3 gigabase genome). made me smile.

    For example, a human egg receives just the genetic information from the father, whilst the mother provides her own genetic material, plus mitochondria and other epigenetic information in a cell that has all the machinery in place for cell growth, division and differentiation. Under the right circumstances, that egg can develop into a fully functioning human being.

    But there is no plan or blueprint encoded in the genome of that egg cell. There is no dimensional information or map of the final layout of the body plan. There is an incomprehensibly (certainly by me, maybe embryologists are beginning to open the door on it) complex interplay of chemicals (translated from genes) such as hormones and other proteins that can block or promote expression of other gene products. So a human being is not a construct in the sense of having been produced from a design plan. For example aspects of limb structure such as bone length are controlled by very few genes. (There is a recent paper on embryological development in bat wings showing how a tiny change in the genome controls finger length which I could track down if anyone is interested.)

    I suspect this is why so many engineers (and practically no scientists) seem to be found in the ID camp, as they fail to grasp how embryology is such an important (and rapidly developing) aspect of biology.

    I lack the time to be more than a sporadic poster, and much appreciate the efforts of others, such as Zachriel, who make such erudite contributions. So, anyone not getting a reply to queries in points raised in my posts, apologies, it is not personal.

    PS to Dave, the two most prominent theorists I know of on abiogenesis are Robert Shapiro and Hubert Yockey, neither of whom have any truck with ID. I have had some email exchanges with Shapiro who takes the view that OOL theories have not scratched the surface of the OOL problem (in particular, he is sceptical of RNA world), and maybe it is insoluble, but that does not lead him to conclude that ID is any form of convincing hypothesis.

  61. Alan Fox says:

    There’s a coincidence!

    P Z Myers has a thread about fins and limbs which illustrates my point about embryology.

  62. […] After sifting through the What Is Science thread, this is where I’m at. […]

  63. […] As it bears directly on this part of the science conversation from yesterday, I thought it might be good to post about it separately. A new computer simulation shows that amid the giant worlds orbiting 55 Cancri, a small rocky world could indeed have formed—in theory—and attracted enough water to support life as we know it. […]

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