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Corante Blogs examine, through the eyes of leading observers, analysts, thinkers, and doers, critical themes and memes in technology, business, law, science, and culture.

The Press Will Be Outsourced Before Stopped

Vin Crosbie, on the challenges, financial and otherwise, that newspaper publishers are facing: "The real problem, Mr. Newspaperman, isn't that your content isn't online or isn't online with multimedia. It's your content. Specifically, it's what you report, which stories you publish, and how you publish them to people, who, by the way, have very different individual interests. The problem is the content you're giving them, stupid; not the platform its on."
by Vin Crosbie in Rebuilding Media

Travels In Numerica Deserta

There's a problem in the drug industry that people have recognized for some years, but we're not that much closer to dealing with it than we were then. We keep coming up with these technologies and techniques which seem as if they might be able to help us with some of our nastiest problems - I'm talking about genomics in all its guises, and metabolic profiling, and naturally the various high-throughput screening platforms, and others. But whether these are helping or not (and opinions sure do vary), one thing that they all have in common is that they generate enormous heaps of data.
by Derek Lowe in In the Pipeline

Disrobing the Emperor: The online “user experience” isn't much of one

Now that the Web labor market is saturated and Web design a static profession, it's not surprising that 'user experience' designers and researchers who've spent their careers online are looking for new worlds to conquer. Some are returning to the “old media” as directors and producers. More are now doing offline consulting (service experience design, social policy design, exhibition design, and so on) under the 'user experience' aegis. They argue that the lessons they've learned on the Web can be applied to phenomena in the physical and social worlds. But there are enormous differences...
by Bob Jacobson in Total Experience

Second Life: What are the real numbers?

Clay Shirky, in deconstructing Second Life hype: "Second Life is heading towards two million users. Except it isn’t, really... I suspect Second Life is largely a 'Try Me' virus, where reports of a strange and wonderful new thing draw the masses to log in and try it, but whose ability to retain anything but a fraction of those users is limited. The pattern of a Try Me virus is a rapid spread of first time users, most of whom drop out quickly, with most of the dropouts becoming immune to later use."
by Clay Shirky in Many-to-Many

The democratisation of everything

Over the last few years we've seen old barriers to creativity coming down, one after the other. New technologies and services makes it trivial to publish text, whether by blog or by print-on-demand. Digital photography has democratised a previously expensive hobby. And we're seeing the barriers to movie-making crumble, with affordable high-quality cameras and video hosting provided by YouTube or Google Video and their ilk... Music making has long been easy for anyone to engage in, but technology has made high-quality recording possible without specialised equipment, and the internet has revolutionised distribution, drastically disintermediating the music industry... What's left? Software maybe? Or maybe not."
by Suw Charman in Strange Attractor

RNA Interference: Film at Eleven

Derek Lowe on the news that the Nobel Prize for medicine has gone to Craig Mello and Andrew Fire for their breakthrough work: "RNA interference is probably going to have a long climb before it starts curing many diseases, because many of those problems are even tougher than usual in its case. That doesn't take away from the discovery, though, any more than the complications of off-target effects take away from it when you talk about RNAi's research uses in cell culture. The fact that RNA interference is trickier than it first looked, in vivo or in vitro, is only to be expected. What breakthrough isn't?"
by Derek Lowe in In the Pipeline

PVP and the Honorable Enemy

Andrew Phelps: "Recently my WoW guild has been having a bit of a debate on the merits of Player-vs.-Player (PvP) within Azeroth. My personal opinion on this is that PvP has its merits, and can be incredible fun, but the system within WoW is horridly, horribly broken. It takes into account the concept of the battle, but battle without consequence, without emotive context, and most importantly, without honor..."

From later in the piece: "When I talk about this with people (thus far anyway) I typically get one of two responses, either 'yeah, right on!' or 'hey, it’s war, and war isn’t honorable – grow the hell up'. There is a lot to be said for that argument – but the problem is that war in the real historical world has very different constraints that are utterly absent from fantasized worlds..."
by Andrew Phelps in Got Game

Rats Rule, Right?

Derek Lowe: "So, you're developing a drug candidate. You've settled on what looks like a good compound - it has the activity you want in your mouse model of the disease, it's not too hard to make, and it's not toxic. Everything looks fine. Except. . .one slight problem. Although the compound has good blood levels in the mouse and in the dog, in rats it's terrible. For some reason, it just doesn't get up there. Probably some foul metabolic pathway peculiar to rats (whose innards are adapted, after all, for dealing with every kind of garbage that comes along). So, is this a problem?.."
by Derek Lowe in In the Pipeline

Really BAD customer experience at Albertsons Market

Bob Jacobson, on shopping at his local Albertsons supermarket where he had "one of the worst customer experiences" of his life: "Say what you will about the Safeway chain or the Birkenstock billionaires who charge through the roof for Whole Foods' organic fare, they know how to create shopping environments that create a more pleasurable experience, at its best (as at Whole Foods) quite enjoyable. Even the warehouses like Costco and its smaller counterpart, Smart & Final, do just fine: they have no pretentions, but neither do they dump virtual garbage on the consumer merely to create another trivial revenue stream, all for the sake of promotions in the marketing department..."
by Strange Attractor in Total Experience

The Guardian's "Comment is Free"

Kevin Anderson: "First off, I want to say that I really admire the ambition of the Guardian Unlimited’s Comment is Free. It is one of the boldest statements made by any media company that participation needs to be central to a radical revamp of traditional content strategies... It is, therfore, not hugely surprising to find that Comment is Free is having a few teething troubles..."
by Kevin Anderson in strange
In the Pipeline: Don't miss Derek Lowe's excellent commentary on drug discovery and the pharma industry in general at In the Pipeline

The Loom

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January 28, 2005

Mutants Today and In Days Gone By

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Posted by Carl Zimmer

Thanks to the many people who left comments on my recent post about some recent work on the intersection of stem cells and human evolution. I noticed that several people expressed variations on the same theme, one which deserves a response. To recap briefly: a great deal of research indicates that a couple million years ago, our hominid ancestors lost the ability to make one of the main sugars that coat mammal cells, called Neu5Gc. This ancient chapter in our history turns out to have a big effect on current research on embryonic stem cells. When human stem cells are raised on a substrate made of mouse cells or calf serum, they absorb the nonhuman Neu5Gc sugars, which ends up on their surface. Humans carry antibodies to Neu5Gc, and these antibodies attack stem cells raised on animal substrates. As a result, existing cell lines fed on this stuff would likely be destroyed if they were implanted in a person.

Some readers questioned whether the research I discussed actually supported evolution and not creationism.

Samuel asked: "If humans are missing this sugar, and the rest of the animal kingdom has it, wouldn't that make humans unique? Could this evidence also support the creationist theory?"

In a similar vein, Graham Mitchell emailed me, writing, "I do find it interesting that you detail how the loss of this sugar in hominids occurred maybe three million years ago and that most other mammals (including primates) still have the sugar, but yet you interpret this evidence as making Intelligent Design *less* likely. As I was reading along, I thought to myself, 'Wow, more evidence that a Designer created humans to be distinct from the animals.'"

I'm happy to respond to these messages, but it's tricky. Neither what Samuel calls "the creationist theory" or what Graham calls "Intelligent Design" offers an explicit hypothesis about how this aspect of our biology came to be. Was mankind created 6,000 years ago without Neu5Gc? Or did a Designer (I'll use Graham's capital D) shut down Neu5Gc 2.5 million years ago in hominid ancestors of humans, with the intent of creating a special species? This is the sort of vagueness that leaves practicing biologists cold when it comes to creationism.

The main point Samuel and Graham are making is that the lack of Neu5Gc appears to be the work of a Designer/Creator who made humans unique from animals. But the lack of Neu5Gc does not actually make us unique. Note that in my original post, I did not say that Neu5Gc is found "in the rest of the animal kingdom," as Samuel put it. I said it was found on every mammal except humans. That's an important difference. The vast majority of animal species--not mention the millions of species of fungi, plants, and bacteria--do not have Neu5Gc. What's more, we have a related sugar called Neu5Ac which all mammals do, and which non-mammals orgnaisms do not.

So our lack of Neu5Gc cannot be interpreted as an example of how the Designer made us unique. On the other hand, there's an obvious (and testable) hypothesis about this evidence that emerges from the theory of evolution. Namely, Neu5Gc and Neu5Ac evolved in the ancestors of living mammals--probably from a similar sugar that can be found on the cells of non-mammals. Then in the human lineage, one of those sugars--Neu5Gc--was lost due to a mutation.

Mind you, evolutionary biologists do not contend that humans are not unique--in the sense that you can scan the human genome and find stretches of DNA not found in any other species. But being unique is not all that...well, not all that unique. A sea slug is also unique, because it also has stretches of DNA not found in any other species. But we would be surprised to hear a sea slug declare that its genetic makeup is evidence that a Designer created it to be distinct from the animals (and not merely because sea slugs are a pretty quiet bunch).

In fact, the study of evolution very much concerned with how humans--and other species--became unique. Evolutionary biologists look at the biology we see around us today and aim to infer how those processes could have produced the diversity of life that surrounds us (and includes us). Some aspects of the history of life are harder than others to study, because there's less evidence at hand. But in the case of Neu5Gc, some things are nicely clear. The gene that makes Neu5Gc in other mammals is not missing from our genomes. It's still sitting there. But right in the middle of it is a distinctive sequence of DNA that belongs to a sort that geneticists understand quite well, called an Alu element.

Alu elements get copied by our cells and those copies get inserted all over our genomes. Scientists can watch the process up close by putting molecular tags on Alu elements in a colony of cells, and then watching it spread over time. In the real world, a fertilized egg may wind up with a new Alu element, which then gets spread to every cell in the baby's body. Out of every 200 births, one child is born with a new Alu element. Sometimes they wind up wedged in the middle of a gene, disrupting its ability to make a protein. In some cases, this leads to a disease. More often, though, the new Alu element ends up somewhere in the genome where it doesn't do much harm. As a result, Alu elements piled up in the ancestors of living humans. The human genome has 1.2 million Alu elements, making up about 10% of its entire sequence of DNA.

Alu elements all work the same way, and all have the same basic genetic sequence. But they are not identical. That's because each time an Alu element gets copied, there's a chance the copying machinery of our cells will make a mistake and introduce a mutation. So Alu elements can be grouped together into families, related by common descent, which in turn can be related to other Alu families. Humans have some unique Alu elements that emerged after we split from other apes, and we also have Alu elements that we inherited from our common ancestor with other apes.

The gene that makes Neu5Gc is interrupted by an Alu element. It's the same Alu element in the same place in the same gene in every person every studied. Scientists can document Alu elements interrupting genes today, either in laboratory experiments or in the maternity ward.

How do we explain this pattern?

On the one hand, there's evolution. The basic idea behind evolution is that mutations have continuously emerged in DNA, leading to variations between individuals in a population. Some of these variations may give individuals an edge in reproducing. If those variations can be inherited, they will gradually become more common. Some populations may split off from the other members of their species and become a new species of their own, but they still carry the adaptive mutations from their common ancestors. And over very long periods of time, many mutations can arise leading to new complex traits.

The case of Neu5Gc is completely consistent with evolution. Scientists may not yet understand what advantage the mutation that robbed us of this sugar had, but the fact that our knowledge is incomplete is not a compelling argument against evolution. After all, scientists don't even know what Neu5Gc andNeu5Ac do today. That doesn't mean the sugars don't exist, or that they aren't important. (As I mentioned before, if you take away these sugars from a mouse through genetic engineering, you end up with a dead mouse.)

Is all of the evidence I've presented consistent with "creationist theory" or "Intelligent Design"? Perhaps someone can offer an explanation that can make it fit, but I don't see it. To create this part of our genome, the Designer would have had to have inserted an Alu element by hand at a particular place in our distant ancestor's genome in order to produce this change. And if Intelligent Design really is supposed to be a scientific theory, that would mean that every time an Alu element winds up somewhere else in the genome, it's the work of a Designer. (You can't just pick and choose the cases that the Designer is responsible for.) And that means that every time someone dies of an Alu-related cancer or other disorder, it's because the Designer invisibly slipped into the body of his or her parents and monkeyed with an egg or a sperm to make sure they died. I look forward to reading the scientific paper documenting that.

Comments (28) + TrackBacks (0) | Category: Evolution


COMMENTS

1. Mark Congdon on January 28, 2005 07:36 PM writes...

"To create this part of our genome, the Designer would have had to have inserted an Alu element by hand at a particular place in our distant ancestor's genome in order to produce this change."

In that statement (and, in fact, throughout your post), you are making the assumption that this change happened through the same genetic processes that we are accustomed to seeing. You assume that the Alu sequence was inserted where we see it in all current humans by a genetic mutation. In fact, you argue by assuming your conclusion.

Now, it is probably the most sensible scientific line of inquiry to think that way. But, it is far from certain, and it is dangerous for you to speak of it as a certainty (note your words: "would have had to have inserted").

Would a simple alternative explanation be that humans did not derive through slow genetic mutations from other hominids, but that at some point, by some process that we cannot imagine or study because it is beyond the scope of our knowledge, a new species was inserted into our world with that genetic difference in place?

I am willing to grant you that this is not a "scientific theory". But neither is it, as you seem to imply, an anti-scientific theory. It is simply a theory that science cannot at this time disprove, and that science can never hope to even try to prove.

Your observations are excellent, except for the certainty with which you state them. It is possible that this evolutionary history, built as it is on less-than-irrefutable evidence, isn't quite right. It is possible that even if all of the fixed points in our evolutionary history are correct, that our ideas of the processes that moved us between them, built as they are on even weaker evidence, are also incorrect.

By all means study, but recognize the uncertainty inherent in what we know so far and are trying to piece together.

Maybe someday we will unearth a group of hominids where this Alu mutation was in the process of moving through the group, and we will be able to see with much more certainty how the process happened. For now, it is conjecture, and it is important for us to speak of it as such.

Permalink to Comment

2. Pericles on January 29, 2005 06:10 AM writes...

To Mark Conqdon,

Your remark:

"Would a simple alternative explanation be that humans did not derive through slow genetic mutations from other hominids, but that at some point, by some process that we cannot imagine or study because it is beyond the scope of our knowledge, a new species was inserted into our world with that genetic difference in place?"

There is no scientific evidence for such a new species "insertion". Your adherence to the proposition is a strong indicator of wishful thinking. In addition you do not address the conclusuion of the final paragraph.

"You can't just pick and choose the cases that the Designer is responsible for.) And that means that every time someone dies of an Alu-related cancer or other disorder, it's because the Designer invisibly slipped into the body of his or her parents and monkeyed with an egg or a sperm to make sure they died. I look forward to reading the scientific paper documenting that."

Mark, you disadvantage yourself by holding onto the idea: "It is simply a theory that science cannot at this time disprove, and that science can never hope to even try to prove."

The journey of a thousand miles starts with a first step. Never say "never"!

The Wright brothers did not accept the advice of those who said "If god had meant us to fly he would have given us wings". You personally benefit from all the advances that science has given us. Electricity for light and heat. The computer you used to post your comments. All the attributes of modern life come from the work of scientists.

You wrote: " Your observations are excellent, except for the certainty with which you state them.

That is intellectual dishonesty. The Pope infamously said to Stephen Hawking that he, Stephen Hawking, could examine the Universe right back to the big bang, but he was not permitted to speculate about before the big bang. What a ridiculous request! As if intelligent people are not going speculate about where we came from?

Back in 2003 "World on fire" by Amy Chua was published. This excellent book on ethnic conflict around the world fails in one major way - Chua doesn't have a clue why some populations (races) are so successful. She fails to understand that populations (races) differ in many behavioral traits, as well as in intelligence and that leads to hostilities in many cases. Amy Chua has assembled the facts, but for what seem to be politically correct reasons, she does not take the final step. It is taboo.

In this world scientific endeavour continually uncovers facts about ourselves that we do not like. Racial prejudice is not nice, yet it would seem it is in our genes. Could genetic engineering eliminate xenophobia? Who knows? Should we try or is genetic research another taboo subject to be banned by the present U.S.president?

The possibilities for humans are vast. Will we achieve them? That is a question for future generations.

Pericles


Permalink to Comment

3. steve on January 29, 2005 10:28 AM writes...

"Would a simple alternative explanation be that humans did not derive through slow genetic mutations from other hominids, but that at some point, by some process that we cannot imagine or study because it is beyond the scope of our knowledge, a new species was inserted into our world with that genetic difference in place?"

Would a simple alternative explanation be that parents did not buy all the presents under the christmas tree, but that at some point, by some process that we cannot imagine or study because it is beyond the scope of our knowledge, a new present was inserted under a tree by a man in a red suit, with a white beard?

Permalink to Comment

4. G Lyn on January 29, 2005 10:43 AM writes...

Mark Congdon states :
"Would a simple alternative explanation be that humans did not derive through slow genetic mutations from other hominids, but that at some point, by some process that we cannot imagine or study because it is beyond the scope of our knowledge, a new species was inserted into our world with that genetic difference in place?"

This is not a theory at all, it is a statement not based on any evidence.

A similar statement would be that the elephants escaped from the local zoo and inserted the Alu elements int all the specimens examined whilst we wer'nt looking - this also cannot be disproved but do you really think it should be given serious consideration ?

We are descended from our parents, who were not identical, and we are not identical to them. We inherited certain characteristics from each of our parents and are different from the offspring of other parents.

This is evolution!

This is Fact!

This is not a theory!

Evolution is fact not theory!

There is a theory of evolution just as there is a theory of light, gravity etc.

Permalink to Comment

5. Carleton Wu on January 30, 2005 01:09 PM writes...

Mark,
First, Carl is not 'assuming his conclusion'. His stated purpose was to explain how the Neu5Gc is consistent with the evolutionary explaination. When attempting to show that process A is consistent with result B, we must start with the assumption that process A exists. That has no bearing on the actual existence of process A, which is an entirely different argument.
That is, all that has been demonstrated is that result B is not evidence against the process of evolution via natural selection.

You are correct in pointing out that it is also not proof of evolution. Likewise, you are correct in asserting that some form of Creationism or ID could explain this result. Furthermore, you are correct in asserting that these processes are not scientific explainations in any way, shape, or form.

It is possible that God created the world 5 minutes ago. It is possible that you're being fed all of this information via direct stimulation of your brain a la The Matrix. It is possible that God has tricked us by creating a universe where consistent physical law appears to be the rule. It is even possible that the elephants are the culprits.

But let us make no mistake- such thoughts cannot be the subject of a rational inquiry. They may be part of a deeply satisfying personal understanding of your place in the world- but they cannot teach us anything, they cannot prove anything, and they cannot predict anything about the objective universe.

Permalink to Comment

6. Invigilator on January 30, 2005 08:52 PM writes...

On behalf of sea-slugity everywhere, I protest! Have we sea slugs ever started a war? Are we not beautiful? Do we not float untrammeled in the sea in all the colors of the rainbow? Why should you humans with your petty concerns and your silly phenomena such as sin, suffering, and belief in several impossible things every day before breakfast consider yourselves superior to us?

You may be superior in the sense that you have done more than any other species in history to destroy our habitat. Proud of that, are you? Makes you feel good? Well, you may be superior in power. Just go ahead and enjoy your miserable existences as well as you can. We'll be around long after you've blown yourselves up!

Permalink to Comment

7. Mark Paris on January 31, 2005 10:52 AM writes...

The creationist argument is fatally flawed simply because it can be changed at will to suit any circumstances. To reduce it to the absurd, one can argue that the Designer created the world in the last instant, with all its "history" intact, including our memories of the past. This is not an idea that any intelligent person needs to spend time to refute. It's time to treat creationism and ID with the contempt they deserve. They are the refuge of the proudly ignorant. Their motto is: "I don't know how this happened, so God must have done it."

Permalink to Comment

8. NuSapiens on January 31, 2005 12:40 PM writes...

As far as I can tell, neither Creationism nor Natural Selection are falsifiable theories. Both have a kind of circular logic that can explain any any event. So technically, both fail the falsifiability test.

However, a key difference is that Natural Selection has been observed by humans many times, while Creationism has never been observed.

Natural Selection also allows people to develop knowledge that empowers humans to participate more fully in life, while Creationism tends to engender a passive approach to the world dominated by a prohibitionist deity.

Permalink to Comment

9. Carleton Wu on January 31, 2005 01:12 PM writes...

NuSapiens,
When you say that 'natural selection' is not falsifiable, I think you need to be more specific. Natural selection is a process, not a theory.

It's like glaciation. Glaciation occurs. After all, we observe glaciers as facts, not theories- ergo, processes must exist that create and maintain them.

But when scientists study a particular area: moraines, erratics, abrasion markings, etc, and conclude that these features were the result of glaciation, then they are creating a scientific theory. A testable theory, in fact, since other evidence might be uncovered, or existing evidence might be reinterpreted in a different light that proves to be a better explaination.
(Something like this actually happened with the great flood in the NW about 12k years ago. Initially the flood signs were thought to be glacial markings, but subsequent investigation desmontrated that they were more consistent with a ice-age damn and subsequent gigantic flood).

Likewise, the use of the process of natural selection to explain certain events is a testable theory. For example, if we could not find any intermediaries between ourselves and the Great Apes, and we found that our genetic code was incompatible with a recent common ancestor (eg many novel genes which had no plausible ancestor in the primate family) we'd have to regard the theory that homo sapiens evolved via natural selection from a Great Ape ancestor as dubious.

Permalink to Comment

10. Jari Anttila on January 31, 2005 07:45 PM writes...

Would a simple alternative explanation be that humans did not derive through slow genetic mutations from other hominids, but that at some point, by some process that we cannot imagine or study because it is beyond the scope of our knowledge, a new species was inserted into our world with that genetic difference in place?

A new species was inserted into our world to look like it was derived through genetic mutations from other hominids. Yes, the simplest alternative explanation to every bit of evolutionary evidence is that somebody staged the whole thing.

I am willing to grant you that this is not a "scientific theory".

It is called omphalism, which is not accepted even by the creationists who want to be taken seriously.

It is simply a theory that science cannot at this time disprove, and that science can never hope to even try to prove.

Science has no need to disprove omphalism, or to take it in any consideration.

Permalink to Comment

11. Mark Congdon on January 31, 2005 08:09 PM writes...

Jari,

I had never heard the word omphalism before... what a delightful word to say. But, I have heard of "apparent age" before, the more common word for omphalism, and that isn't what I was suggesting.

In your comment, you characterized my position thus: "A new species was inserted into our world to look like it was derived through genetic mutations from other hominids." Actually, I suggested the possibility that a new species was inserted into our world... end of sentence.

Now, I'm not a scientist, but I haven't seen anything that I've read on this issue that makes it "look like" our change was derived through genetic mutations. That might be the most reasonable scientific guess so far, but it is certainly a guess still based on the evidence.

That's the extent of my point... the full extent of my point. The evidence we have so far does not warrant the strength of the conclusions that you are drawing.

You are stating in effect that the evidence that we see of these sugars "looks like" genetic mutations from other hominids so strongly that we can take that to be the case. I disagree. The evidence of these sugars shows a consistent difference between humans and other mammals, but does not give us strong reason to suppose how that difference came about. Genetic mutation may be the best idea to date, and the one we should focus our research on, and maybe someday it will be proven accurate... but there are significant difficulties with it yet, and it is unwise to jump to presumptuous conclusions.

Mark

Permalink to Comment

12. Pericles on February 1, 2005 06:47 AM writes...

Mark wrote:
"Now, I'm not a scientist, but I haven't seen anything that I've read on this issue that makes it "look like" our change was derived through genetic mutations."

As they say in Scotland "Ye nae have read enough, laddie"

Go to Gene Expression http://www.gnxp.com/ and start reading.

Pericles

Permalink to Comment

13. js on February 1, 2005 01:35 PM writes...

Just as a note, the online definition of omphalism (in the "obscure words" site) is wrong or incomplete at best.
Omphalos is navel. You can do the derivations from there (but the offered definition of "centralized government" is misleading at best).
Mark- Don't you see why this line of argument you're bringing is flawed?
Think of this as an example. We are sitting next to each other, alone in the room. Suddenly, while you're looking away, you feel a smack on the back of your head. You look back at me and say "Why did you smack me?"
I say "I didn't do it. God did."
Do you believe me? You didn't see me do it, so you can't prove it. But, you've seen me smack other people, often for presenting spurious arguments. And again, there was no one else there and you distinctly felt what you believe to be my hand on the back of your head.
You decide to call an authority, perhaps our boss or some police officer. I say "But Mark, really, you can't prove that I hit you. You can prove that it was very likely that I hit you. But I don't think the evidence supports the certainty of your conclusions. Remember, God is all powerful. To say that He could not have smacked you in the head is to deny his power."
Do you see what I'm getting at? Or do you need to have your head smacked by God before it becomes clear?

Permalink to Comment

14. Mark Congdon on February 1, 2005 01:54 PM writes...

Pericles,

Thank you for the link. I will begin reading. I was hoping someone here might be able to point out the missing evidence in layman's terms, but the responses have generally missed the point of what I'm saying completely.

js,

Your example, like the Santa Claus example before, over-simplifies the situation. If the evidence was so obvious that genetic mutations over long periods of time were the cause of, say, the Neu5Gc difference between humans and other mammals, then your story would have good basis.

But, in reality, I think it goes more like this. We are sitting alone in a room together, but you're 15 feet away from me. I look away, feel a smack on the back of my head, and turn back. You're still sitting 15 feet away from me. There isn't any good explanation for how that happened, but the "you hit me" explanation is the most reasonable. Still, there are serious holes and uncertainties about it, and I have to take into account the possibility that something may have happened that I can't account for.

I'm a skeptic, a careful thinker, even a methodical thinker at times. I hope that someday we'll find, as I suggested, a community of humans or hominids in the skeletal record that have this particular gene mutation in process. That would certainly increase our certainty about this particular situation.

Until something like that, I don't think it is foolish of me to reserve judgment, recognize the weaknesses in the evidence so far, and hope for more clarity in the future.

It is surprising to me that I have generated such heated responses here from what seems to me to be such a simple observation and conclusion. This is, undoubtedly, an emotionally-charged issue.

Mark

Permalink to Comment

15. Jari Anttila on February 1, 2005 08:31 PM writes...

Mark wrote:

In your comment, you characterized my position thus: "A new species was inserted into our world to look like it was derived through genetic mutations from other hominids."
....
You are stating in effect that the evidence that we see of these sugars "looks like" genetic mutations from other hominids so strongly that we can take that to be the case. I disagree. The evidence of these sugars shows a consistent difference between humans and other mammals, but does not give us strong reason to suppose how that difference came about.

Read again what Carl wrote:
"The gene that makes Neu5Gc in other mammals is not missing from our genomes. It's still sitting there. But right in the middle of it is a distinctive sequence of DNA that belongs to a sort that geneticists understand quite well, called an Alu element.
Alu elements get copied by our cells and those copies get inserted all over our genomes
....
Sometimes they wind up wedged in the middle of a gene, disrupting its ability to make a protein."

It sure looks like a genetic mutation to me. If it's not, then what is the Alu-looking sequence doing there? If the human Neu5Gc gene was only made to look like it was disabled by an Alu, then that's omphalism, like the "apparent age" case. And why do we have the defunct Neu5Gc gene at the first place?

If some intelligent designer or breeder, instead of natural evolution, used the Alu element to disable the gene later, then that's the same thing as a mutation from earlier hominids. The humans before the mutation were "earlier hominids".

The human genome has several features that apparently have no other function than to make us believe in common descent between the primates:
Constructing primate phylogenies from ancient retrovirus sequences

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16. triticale on February 6, 2005 10:45 AM writes...

The entire genomic structure is full of nifty structures for the propogation of mutation, some of which actively promote successfull ones. I postulate a Designer Who, after setting up this complex structure, wound it up, pointed it in a direction, and turned it loose, perhaps to see what happened. This concept does not by the way, preclude the possibility of stopping back once in a while and applying a tweak or two (even if I am not allowed to pick and choose which changes were deliberate). I do not hold strong belief in this, but find it aesthetically pleasing. Aside from everthing else, if we are not the only such project, it would explain the racial patterns exhibited in Star Treck.

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17. Ginger Yellow on February 6, 2005 04:56 PM writes...

Mark: read what Carl wrote again. We know, through manipulating the genes of and observing mice, that genetic mutation can cause Neu5Gc to disappear. We know, through observation of humans, that the gene that codes for Neu5Gc is present in humans, but deactivated by a product of genetic mutation. Exactly the same product of mutation in every single human ever studied. Do you disagree with any of that? If not, how can you honestly say that the evidence does not suggest that the lack of Neu5Gc in humans is the result of a genetic mutation in a common ancestor? Of course that's what it looks like.

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18. Mark Congdon on February 7, 2005 01:55 AM writes...

Ginger Yellow,

You wrote: "We know, through observation of humans, that the gene that codes for Neu5Gc is present in humans, but deactivated by a product of genetic mutation." You have, in that statement, assumed your conclusion. We should more accurately say it was "inactive because of a genetic difference that could well have been caused by a genetic mutation."

I am happy to say that the evidence "suggests" a genetic mutation through evolutionary processes, and that it "looks like" that. No argument here, never has been. But, our knowledge of this topic (and, in particular, our direct evidence) is still limited enough that I think we should maintain a healthy degree of uncertainty in our language.

It was, primarily, the certainty (and even disdain of other views) exhibited by Carl Zimmer that I felt deserved a comment.

Mark

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19. Ginger Yellow on February 7, 2005 03:37 AM writes...

That's not what you said before. Quote: "You are stating in effect that the evidence that we see of these sugars "looks like" genetic mutations from other hominids so strongly that we can take that to be the case. I disagree." Given that the only other theory suggested is that something inserted a new species into the ecosystem, cunningly designed to look like the result of genetic mutation, all of which is a process that has never, ever been observed, I think Carl's certainty is justified. Unless you want to argue that if it looks like a duck, walks like a duck, and quacks like a duck, it might be a cunningly disguised elephant.

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20. MakeMineRed on February 7, 2005 05:05 PM writes...

Mark:

You wrote "It is surprising to me that I have generated such heated responses here from what seems to me to be such a simple observation and conclusion. This is, undoubtedly, an emotionally-charged issue."

You brought forth your argument politely; others brought theirs to counter yours in a civil fashion, and you have responded in turn. Any heat or emotional charging is a perception on your part, one which says much about you.

MakeMineRed

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21. Jari Anttila on February 7, 2005 05:55 PM writes...

Mark:

We should more accurately say it was "inactive because of a genetic difference that could well have been caused by a genetic mutation."

Would you accept this:
"inactive because of a genetic difference that as far as we know has been caused by a genetic mutation" ?

I can't think any other way to make a difference between a real mutation and an apparent mutation like this than to get a time machine.

I am happy to say that the evidence "suggests" a genetic mutation through evolutionary processes, and that it "looks like" that. No argument here, never has been.

Good to know it now.

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22. Mark Congdon on February 7, 2005 06:06 PM writes...

Ginger Yellow,

Your quote of me agreed exactly with my previous statement, and did not contradict at all. It is my "so strongly" statement that you disagree with. I dispute that the evidence is strong enough to support certainty. You believe that it is. In no case is it fair to say, "That's not what you said before".

MakeMineRed,

With respect to many responses, you are correct. However, js, the poster directly before I made that comment, ended his post with the wonderfully respectful statement: "Do you see what I'm getting at? Or do you need to have your head smacked by God before it becomes clear?" G Lyn's response was another example of completely exaggerating my statements, then ridiculing the straw man of "Evolution is a Theory" which I had never proposed. I stand by my characterization, while granting you that it was not universal. :)

Mark

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23. Steve Russell on February 8, 2005 02:34 PM writes...

Mark, now that we get (what I take to be your point) that the claims of the evolutionists to have adequately "explained" certain phenemena is open to criticism, I don't get what you would like to see done about it.
Once you have acknowledged, as I THINK you have, that creationism and ID aren't scientific theories and don't generate testable claims or predictions, it's not clear what you think we are left with.
On the one hand, we have evolution, which--at least at your current level of review of the literature--seems not to meet your still-rather-nebulous "standard of proof." Testing of the theory can--and will--proceed, and discussion of the level of proof required can continue to take place. That's going to happen with or without you.
Then we have ID/creationism, which you appear to concede don't make testable claims and aren't science. Any contentions from that direction, therefore, would have to be taken on "faith," right?
But where do we go from here? Do we abandon the effort to make some kind of testable sense out of the patterns of nature, and just believe whatever we want--to the arguable detriment of progress in medicine, biology, molecular chemistry, etc?
Do we substitute, for science's proven power to "evolve" workable and useful explanations (even if they are never "final"), whatever faith-based beliefs people can dream up for the physical phenomena that puzzle them?
What's not clear to me is the usefulness of the debate you have framed. Or whether you have even framed a debate. It is of course your "right" to ignore or critique the quality of the evidence supporting a given evolutionary explanation. But where does a faith-based explanation fit in your scheme of things? Should such an "explanation" be pursued by "scientists" even in the total absence of anything like the weight of proof (whether you deem that weight to be heavy or light) generated by the evolutionists? How do you weigh something against nothing? Should ID and creationist (or other faith-based) explanations be taught in schools as "alternatives" to evolution? Shouted from the pulpit? What is their appropriate role, if any, in your critique of evolutionism?
You seem uncomfortably suspended between two extremes, questioning the proof of evolutionary theory, admitting that ID/creationist/faith-based explanations AREN'T science and AREN'T testable, but somehow impliedly favoring the latter over the former. Does ANY degree of (alleged) uncertainty in the quantum of scientific proof require us to just junk the whole rational enterprise? Does any such uncertainty then fling open the doors to any imaginable explanation in which someone chooses to have faith?
There are places humans need to go in life, and things they need to think about, where I might agree with you that we have no other guide than a thoughtful faith. But what--in your mind--is the appropriate role of "faith" in trying to explain a given "difference" between human and non-human sugar-specifying stretches of DNA? What's the role of "faith" in trying to figure out why a mole of one species has a suuper-sensitive star organ, and another does not?

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24. Mark Congdon on February 8, 2005 05:49 PM writes...

Steve,

I have no concern with science, how it is being performed, what research is being done, etc. That has not been what I have presented here from the beginning.

But, most of us are not scientists presenting scientific hypotheses. Most of us are professionals in other fields, thinkers who are evaluating the claims of science from a distance.

Most people (and in this case I was specifically referring to specific ways Zimmer communicated in this article) seem very quick to state either that evolution is an idiotic view held up only by ideological atheism, or that evolution is an obvious proven fact that only an ideological religious freak could question. I believe there is quite enough uncertainty in our evidence so far to make it possible for someone to be unconvinced about evolution without therefore being ideological; and I think there is enough evidence of evolution to make it possible for someone to be convinced of the truth of evolution with therefore being ideological.

I would recommend that we (on all sides of this discussion) try to maintain that respect for different views, and recognition of uncertainty, in our language.

You seem to feel that I have said far more than that, that I am advocating that science incorporate faith, or that we throw out science, or something drastic. I suggest nothing of the sort. I hope I make a little more sense to you now...

Mark

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25. Steve Russell on February 8, 2005 06:50 PM writes...

Mark, what has confused some of the rest of us is your proposing the "insertion of a species [bearing a gene sequence carefully-designed to mimic the appearance of a mutation]" as if it were a reasonable alternative. I didn't go all the way back to the other thread to grab a copy of your words, but you seem not to have objected to the quote above, which I re-quote here:

"Would a simple alternative explanation be that humans did not derive through slow genetic mutations from other hominids, but that at some point, by some process that we cannot imagine or study because it is beyond the scope of our knowledge, a new species was inserted into our world with that genetic difference in place?"

This sure made it sound like you were coming at this from an "ideological" perspective, since--as the other commentators have now beaten to death--however "simple" such an "alternative explanation" may sound, it is neither an alternative--in the sense of an alternate "scientific" theory--nor is it an explanation, since it doesn't "explain" anything, or offer any way to get a grip on using the gene sequence observation to accomplish anything else useful in the world. Nor, very frankly, did this serve as any kind of a meaningful critique of Zimmer's reasoning.

As you revisited the issue, you seemed to grasp something of the nature of the problem, and you confined your comments to more general concerns about the "circularity" of Zimmer's reasoning and the tenor and tone of the dabate. Whether or not I agreed with these reframings of your concerns, I at least understood them.

I don't think anybody has a problem with intelligent lay people--whether they style themselves as people "of faith" or not--choosing not to get caught up in some of the excesses of emotion that flare along the front lines of this debate. But simply because the two sides in a debate have staked out extreme positions does not automatically render both sides "extremeists." Nor does it rule out the possiblity that one side has it closer-to-right than the other.

It's at least possible that this is a debate that could have larger consequences for the pursuits of both science and religion in our world, and for the appropriate role that each way of understanding life's mysteries should play. In short, the day may come--sometime short of Judgment Day!--when picking a side in this debate could be the kind of decision that "informed" lay people should not stand aside from.

It's also possible that the evolutionists really are closer to getting at least the small answers to the small questions right--why the star mole's star? why this particular gene sequence in humans and not in nonhuman primates?--than are the creationists.

How do we go about judging such things? While your slap-upside-the-head analogy is a rough and ready, rule-of-thumb, seat-of-the-pants way to think about--and even decide, in realtime--certain kinds of everyday problems, it does not afford any sort of a well-honed way to approach many other kinds of troublesome issues that the world can throw at us. It does not substitute, in my view, for a meaningful grasp of how science proceeds.

At some point, a hands-off, let-the-rowdies-fight-about-it stance may not suffice. I would feel better knowing that, while you are out there pursuing your livelihood and deepening your faith, you are also educating yourself in at least the generalities of how science collects and evaluates evidence. Maybe at that point you will revisit this issue. I, for one, would be interested to hear from you at that point.

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26. Mark Congdon on February 9, 2005 03:35 PM writes...

Steve,

You now seem to have come to the conclusion that I propose that scientists worry about science, and the rest of us should just stop paying attention. I'm confused how you came to that conclusion about me.

But, as this has just become an exercise in you trying to understand me personally, and me trying to explain myself to you (with very limited success), and since we don't have a relationship that extends beyond this thread, I figure it's not worth the effort.

Thanks for your input, and I hope we can part with no hard feelings.

Mark

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27. Steve Russell on February 9, 2005 04:40 PM writes...

Oh, Mark, absolutely!

And, actually, I find your comments in response to the latest input on this issue on your own blog rather open-minded and refreshing, so I'm content to shut up here...with the parting remark that it's pleasant to have dialogued on this issue with a non-fanatic, even if we did manage to keep sliding by each other's points.

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28. MakeMineRed on February 14, 2005 05:05 PM writes...

Mark: you said

With respect to many responses, you are correct. However, js, the poster directly before I made that comment, ended his post with the wonderfully respectful statement: "Do you see what I'm getting at? Or do you need to have your head smacked by God before it becomes clear?"

Perhaps you missed the metaphor which spawned that sentence. Sure, it allowed js the opportunity to tweak you. It's not as if you haven't tweaked others in this exchange.

You also said:

G Lyn's response was another example of completely exaggerating my statements, then ridiculing the straw man of "Evolution is a Theory" which I had never proposed.

Granted, he used exclamation points, but he never said that you had erected a straw man. And your interpretation of exaggeration on his part is quite wrong. Look - your argument of insertion of a species is a non-starter. It can't go anywhere; there's nothing anyone can do with it. It's absolutely equivalent to G Lyn's example of elephants changing Alu elements. Your argument says that any species can be inserted anywhere at any time. Why, then, would it matter in this particular instance? Or at all?

MakeMineRed


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