Here. Since there is very little evidence the blind watchmaker can do that much without help from proteins, the next question to ask is: why are proteins so incredibly helpful to the blind watchmaker?
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May 6th, 2008 at 11:59 pm
Wow! You ask tough questions. Here's some research that might help provide some answers.
http://www.proteomonitor.com/i...
May 1, 2008
The Human Proteome Organization plans to launch an ambitious initiative to map the entire human proteome, a project that is anticipated to last up to a decade and cost $1 billion.
In an interview with ProteoMonitor last week, John Bergeron, immediate past president of HUPO and a professor of anatomy and cell biology at McGill University, broadly outlined the goals of the initiative, called the Human Proteome Project, which HUPO began thinking about in 2006.
Comment by nobody — May 6, 2008 @ 11:59 pm
May 7th, 2008 at 2:20 pm
The blind watchmaker exists whether there is life or not, and whether there are proteins or not.
Consider the lowly rock.
With the blind watchmaker's help, rocks replicate imperfectly. They divide, and recombine constantly. They can even catalyze the formation of new and different kinds of rocks, with different and complex morphology and compositions. They react chemically with one another, and some rocks (magnetic) even can learn and remember. Some other rocks (uranium ore) have the ability to "metabolize" (radioactive decay), producing "waste" (lead) and energy (heat, radiation) that can facilitate the production of offspring (other composites). Rocks are beautiful. Some glow, some sparkle, some can burn with fire, some can attach to one another in crystalline perfection, much the way amino acids attach to one another.
One might even say that from one or a few original forms, rocks have grown into endless forms most beautiful and most wonderful.
I know rocks seem slow and dumb compared to your fancy fast acting proteins, but aren't we all just a bunch of chemical compounds sloshing through the universe? Who's to say that todays rock couldn't become a flying mineral organism in a few billion years of tinkering? Doesn't the blind watchmaker tinker with rocks the same mindless lack of forethought with which he constructs the mighty bald eagle?
In other words, can you qualify what makes a squirrel and bug ridden ash tree any different from a majestic erupting volcano, from the perspective of a blind watchmaker?
Comment by chunkdz — May 7, 2008 @ 2:20 pm
May 7th, 2008 at 5:35 pm
Hey Mike,
Science doesn't usually answer questions that start with why. It normally deals with how.
Comment by olegt — May 7, 2008 @ 5:35 pm
May 7th, 2008 at 5:44 pm
Science doesn't. But folks posting on blogs dealing with telic thoughts might.
Comment by hrun — May 7, 2008 @ 5:44 pm
May 7th, 2008 at 5:51 pm
Mike:
It's hard to understand the question without knowing which word is emphasized. Why are proteins [as opposed to some non-protein substances] so… or why are proteins so incredibly [as opposed to, say, moderately] helpful… or why are proteins so incredibly helpful [as opposed to, say, detrimental] to…
Comment by Raevmo — May 7, 2008 @ 5:51 pm
May 7th, 2008 at 5:56 pm
Well you're not saying much then by utilizing words like "usually" and "normally".
Say someone provides cases in which scientific theories were centered around the "why" you could simply respond, "but I only said 'usually'".
Either way, phenomonological theories tend to be generalizations off of recorded date and explanatory theories attempt to delve deeper, not simply generalizing from the data.
Comment by Doug — May 7, 2008 @ 5:56 pm
May 7th, 2008 at 6:08 pm
I can state it in the more categorical form, Doug.
Science doesn't deal with the why, it deals with the how.
Now could you give me an example of an explanatory theory so that I better understand what you mean? Thanks.
Comment by olegt — May 7, 2008 @ 6:08 pm
May 7th, 2008 at 7:05 pm
Placing a why in a question does not make it scientifically irrelevant. The why in the blog entry references the blind watchmaker- imagary for mainstream evolution. A why question would be why are there atoms. Asking why proteins facilitate evolution is a good means of introducing discussions of mechanisms and the hows of them.
Comment by Bradford — May 7, 2008 @ 7:05 pm
May 7th, 2008 at 7:14 pm
olegt:
Well, I can deal with "why." Why do you suppose science (in its evo-psych cum sociobiology form) so often tell us that fish have fins because they swim, birds have wings because they fly, etc., etc. Why are giraffe's necks long? To feed on upper foliage nobody else can reach, of course. Why do humans have trichromatic vision? To find ripe fruit/know when a girl's in heat/know when someone's embarrassed/know when blood is flowing, of course. (this particular story changes regularly depending on whose report on why is the subject this week).
Not exclusive to evo-psych, since we read this sort of crap all the time in the science press reports about evolutionary explanations for this or that. Obviously science DOES deal with "why." That it's supposed to be outside proper scientific purview by definition has never stopped evolutionary biologists from asserting their work as sure knowledge of "why."
Comment by Joy — May 7, 2008 @ 7:14 pm
May 7th, 2008 at 7:38 pm
Sure science can ask why-questions. Why is a polar bear white? It's the same as asking how did it happen that polar bears are white? The question can haz multiple meanings.
http://en.wikipedia.org/wiki/T...
Comment by Raevmo — May 7, 2008 @ 7:38 pm
May 7th, 2008 at 8:40 pm
Raevmo,
There is a difference, I think. In the how form, your question is a summary of a concrete research proposal: determine the evolutionary path from brown bears to polar bears. The why form suggests an underlying purpose. It sounds like one is interested not in determining the evolutionary history but rather in finding the reason for the divergence between brown and polar bears. Why did that brown bear took a wrong turn and ended up near the polar circle? We may never know.
Comment by olegt — May 7, 2008 @ 8:40 pm
May 7th, 2008 at 9:17 pm
Hi olegt,
Indeed. But so what? Did I assert somewhere that I was doing science?
Comment by MikeGene — May 7, 2008 @ 9:17 pm
May 7th, 2008 at 9:18 pm
Hi hrun,
Nothin' wrong with that. What matters is whether the question is thought-provoking, not how we classify it.
Comment by MikeGene — May 7, 2008 @ 9:18 pm
May 7th, 2008 at 9:21 pm
Hi Raevmo,
Argument by Nitpick. Are you under the impression that your comments and questions cannot be nitpicked? What does he mean by "understand?" What does he meaning by "knowing?" What does he mean by "emphasized?" And where or where is the emphasis in his comment?
Games.
Comment by MikeGene — May 7, 2008 @ 9:21 pm
May 7th, 2008 at 9:32 pm
MikeGene wrote:
There already is one Thought Provoker in these quarters. Think we need more?
Comment by olegt — May 7, 2008 @ 9:32 pm
May 7th, 2008 at 9:36 pm
Olget
Because that's where the seals were
Comment by fifth monarchy man — May 7, 2008 @ 9:36 pm
May 8th, 2008 at 11:04 am
Dalton trying to explain why atoms bound to each other in fixed ratios. This lead to his conception of the atomic theory, as well as his belief that atoms connected to other atoms via little hooks.
Comment by Doug — May 8, 2008 @ 11:04 am
May 8th, 2008 at 11:21 am
olegt:
I can see how it might be confusing, but why-questions in biology usually refer to functionality or adaptive value of a trait. Why are polar bears white rather than brown or some other color? Answer (hypothesis): white is (in some sense) the best camouflage. The research proposal might then include experimentally painting polar bears brown to see how that affects their hunting success.
Comment by Raevmo — May 8, 2008 @ 11:21 am
May 8th, 2008 at 11:33 am
Mike:
Argument by Argument by Nitpick. I'm trying to figure out what you mean by the question. It's obvious that proteins can perform many functions. Are you saying that a different kind of polymer (with building blocks other than amino acids or perhaps different amino acids) would be less helpful? Can we say that proteins are optimal in some sense, compared to other kinds of polymers? Such considerations must have been made by The Frontloader, don't you agree?
Comment by Raevmo — May 8, 2008 @ 11:33 am
May 8th, 2008 at 11:42 am
Raevmo says.
Right. You may go first with that idea about "research".
Comment by nobody — May 8, 2008 @ 11:42 am
May 8th, 2008 at 11:49 am
nobody:
No thanks, but how would you demonstrate that whiteness of polar bears is adaptive?
Comment by Raevmo — May 8, 2008 @ 11:49 am
May 8th, 2008 at 11:59 am
That's what grad students are for.
Comment by Zachriel — May 8, 2008 @ 11:59 am
May 8th, 2008 at 12:06 pm
Zachriel:
You got it. When I was a grad student they made me climb to goshawk nests. I've you've ever seen an angry goshawk mother, painting a polar bear brown seems like a walk in the park (provided the bear being sedated).
Comment by Raevmo — May 8, 2008 @ 12:06 pm
May 9th, 2008 at 4:09 pm
A question, Mike Gene. and I know it may seem unrelated to the topic, but it is inspired by you and a brief conversation I had with Stephen Jay Gould more than thirty years ago:
Does phylogeny recapitulate ontogeny?
Is that what you're trying to tell me?
Comment by Rock — May 9, 2008 @ 4:09 pm
May 9th, 2008 at 4:37 pm
I thought he was saying that technology recapitulates phylogeny.
Comment by chunkdz — May 9, 2008 @ 4:37 pm
May 9th, 2008 at 6:02 pm
Hi Rock,
Not quite. There are many differences between ontogeny and phylogeny. The former occurs over a short time, in a controlled environment, and does not require the creation of new genes. The latter occurs over a very long time, in an ever-changing world, and requires the creation of new genes.
I suppose I'm thinking more along the lines that phylogeny echoes ontogeny.
Comment by MikeGene — May 9, 2008 @ 6:02 pm
May 9th, 2008 at 11:15 pm
olegt Says:
Why is the sky blue?
Comment by nobody — May 9, 2008 @ 11:15 pm
May 10th, 2008 at 6:13 pm
I don't recall what specifically we discussed, but Gould referred me to Schindewolf's "Basic Questions" (which Gould resurrected for the nth time and wrote the Foreword to some 20 years later–something always on his mind?).
Very interesting ideas. Check it out and tell me what you think.
(While checking for a proper citation on the Web I noticed that Schindewolf is a darling of the creationists–who, as usual, don't seem to ever "get the point.")
Comment by Rock — May 10, 2008 @ 6:13 pm
May 11th, 2008 at 7:52 pm
Hi Raevmo,
I'm not sure why you are confused. Perhaps it would help if you simply tried to answer the questions I originally posed:
Without proteins, would there be a Tree of Life 3.5 billion years after the
RNA world took root? How do we know? If we believe so, would the Tree be
as immense and vast as it is today? A life form composed of nucleic acids,
carbohydrates, and lipids would suffice for the purposes of the blind
watchmaker. But could the blind watchmaker turn this material into
something that is analogous to an Ash tree filled with squirrels, beetles,
and birds?
Comment by MikeGene — May 11, 2008 @ 7:52 pm
May 11th, 2008 at 8:04 pm
I'll give it a shot.
Yes. We don't. Even bigger. No.
Comment by hrun — May 11, 2008 @ 8:04 pm
May 11th, 2008 at 8:07 pm
Hi hrun,
Thanks. Can you now explain your answers?
Comment by MikeGene — May 11, 2008 @ 8:07 pm
May 12th, 2008 at 9:20 am
Mike:
OK, maybe that helps.
Yes.
We don't know - it's just a guess. Instead of proteins, some other polymer might have evolved, not based on amino acids.
Maybe less vast, maybe vaster.
What are the purposes of the blind watchmaker, and why would nucleic acids, carbohydrates and lipids suffice for that? Why not just nucleic acids for example?
Anyway, a world without proteins did presumably once exist, and then it evolved into a world with proteins. First with a simple genetic code and small set of amino acids, later with a more complicated codes and more amino acids.
Comment by Raevmo — May 12, 2008 @ 9:20 am
May 12th, 2008 at 11:19 am
Raevmo,
No it didn't.
Comment by chunkdz — May 12, 2008 @ 11:19 am
May 12th, 2008 at 11:45 am
chunkdz:
I see. And you know this how?
Comment by Raevmo — May 12, 2008 @ 11:45 am
May 12th, 2008 at 11:51 am
"…it's just a guess."
Comment by chunkdz — May 12, 2008 @ 11:51 am
May 12th, 2008 at 12:01 pm
No disagreement there
Comment by Raevmo — May 12, 2008 @ 12:01 pm
May 12th, 2008 at 12:32 pm
Raevmo,
It was probably for your own good.
Comment by chunkdz — May 12, 2008 @ 12:32 pm
May 12th, 2008 at 12:45 pm
Raevmo
There you have it folks. If proteins had never formed, the tree of life would have been made of polyester.
Comment by chunkdz — May 12, 2008 @ 12:45 pm
May 12th, 2008 at 3:17 pm
Indeed. We've hit the metaphysical nerve.
Comment by MikeGene — May 12, 2008 @ 3:17 pm
May 12th, 2008 at 3:42 pm
And why wouldn't they. The Polyesters are a highly diverse group of polymers, some of naturally occurring in plants. Do you think we have any sense of the diversity that polyesters can have? Maybe you are thrown off by the rather mundane functions of commonly know polyesters, like for example polyethylene terephthalate. Since PET is a polymer that consists only a single monomer, one would not expect it to have a particular diverse range of possible functions. That would be like just looking at polylysine when trying to figure out the possible functions of proteins.
How so? Because Raevmo and I believe there could be very functionally diverse polymers other than proteins?
Comment by hrun — May 12, 2008 @ 3:42 pm
May 12th, 2008 at 4:03 pm
Is there any science behind your belief?
Comment by nobody — May 12, 2008 @ 4:03 pm
May 12th, 2008 at 4:11 pm
Nope. Just conjecture. But I figured that Mike wanted an answer to his question. Obviously, the right answer is 'Nobody knows at this point.' about any of his questions posed.
But remember that Mike said: "I'm not sure why you are confused. Perhaps it would help if you simply tried to answer the questions I originally posed:"
So I guess both Raevmo and I gave it a shot. Did it help?
Comment by hrun — May 12, 2008 @ 4:11 pm
May 12th, 2008 at 4:18 pm
hrun,
Maybe they could.
They are incredibly versatile.
Maybe you are thrown off by your preconceptions. Personally I think polyesters are a fine candidate for an evolutionary medium. But then again, I think rocks evolve.
Comment by chunkdz — May 12, 2008 @ 4:18 pm
May 12th, 2008 at 4:23 pm
Way to go on keeping the discourse going.
What would your answers be to Mike's questions? Would your answers also indicate that a metaphysical nerve was hit?
Comment by hrun — May 12, 2008 @ 4:23 pm
May 12th, 2008 at 4:37 pm
Indeed, as it is a belief about something that could be that in turn is rooted in metaphysics, not evidence. Thus, when you conjecture that other materials could easily substitute for proteins, it is no more valid than my conjecture that proteins are not superfluous to evolution. Either position can then influence the way we perceive and interpret evolution.
Of course, the advantage to my position is that we have abundant evidence to indicate that proteins have played crucial roles in evolution and these can be explored. And it also calls into question any attempt to extrapolate protein-dependent evolution to protein-less evolution. Claims about protein-less evolution should be supported by independent evidence.
Comment by MikeGene — May 12, 2008 @ 4:37 pm
May 12th, 2008 at 4:43 pm
hrun
I didn't answer them because I rejected Mike's original premise:
Personally, I think the blind watchmaker does amazing things with inanimate material. Mike's premise only makes sense if you only consider animate objects to be superior to the inanimate. The blind watchmaker could not care less. He tinkers with what he's given, takes no joy in the outcome, and has no goals or foresight.
So what if life was polyester based? Why would a blind watchmaker find this any better to work with than simple raw minerals? He's just as happy making stalactites grow.
Comment by chunkdz — May 12, 2008 @ 4:43 pm
May 12th, 2008 at 5:07 pm
MikeGene says:
That's true. In fact, you reminded me of what Carl Sagan said:
Comment by nobody — May 12, 2008 @ 5:07 pm
May 13th, 2008 at 9:40 pm
Folding Proteins on Your Lunch Break. Pretty neat, though the site where you fold it (www.fold.it) is down for maintenance.
Comment by todd — May 13, 2008 @ 9:40 pm